Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| 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 |
| sponge-associated microorganisms: evolution, ecology, and biotechnological potential. | marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. in some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). we review in detail the diversity of microbes associated with sponges, including extensive 16s rrna-based phylogenetic analyses which support the previously suggested existence of a spong ... | 2007 | 17554047 |
| the relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. | the distribution of isoelectric point (pi) of proteins in a proteome is universal for all organisms. it is bimodal dividing the proteome into two sets of acidic and basic proteins. different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size. | 2007 | 17565672 |
| 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 |
| comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. | folate synthesis and salvage pathways are relatively well known from classical biochemistry and genetics but they have not been subjected to comparative genomic analysis. the availability of genome sequences from hundreds of diverse bacteria, and from arabidopsis thaliana, enabled such an analysis using the seed database and its tools. this study reports the results of the analysis and integrates them with new and existing experimental data. | 2007 | 17645794 |
| bphyog: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes. | overlapping genes (ogs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. with the rapid accumulation of sequence data, many ogs in bacterial genomes have now been identified. indeed, these might prove a consistent feature across all microbial genomes. our previous work suggests that ogs can be considered as robust markers at the whole genome level for the construction of phylogenies. an online, interactive web server for inferring phyloge ... | 2007 | 17650344 |
| evolution of ribonuclease h genes in prokaryotes to avoid inheritance of redundant genes. | a theoretical model of genetic redundancy has proposed that the fates of redundant genes depend on the degree of functional redundancy, and that functionally redundant genes will not be inherited together. however, no example of actual gene evolution has been reported that can be used to test this model. here, we analyzed the molecular evolution of the ribonuclease h (rnase h) family in prokaryotes and used the results to examine the implications of functional redundancy for gene evolution. | 2007 | 17663799 |
| identification of genes encoding trna modification enzymes by comparative genomics. | as the molecular adapters between codons and amino acids, transfer-rnas are pivotal molecules of the genetic code. the coding properties of a trna molecule do not reside only in its primary sequence. posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. despite a wealth of biophysical and structural knowledge ... | 2007 | 17673083 |
| 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 |
| selection against spurious promoter motifs correlates with translational efficiency across bacteria. | because binding of rnap to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of dna motifs capable of rnap-binding across the genome. here we analyze the distribution of the -10 promoter motifs that bind the sigma(70) subunit of rnap in 42 bacterial genomes. we show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequ ... | 2007 | 17710145 |
| 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 |
| is transcriptional regulation of metabolic pathways an optimal strategy for fitness? | transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. the lac operon of e. coli is but one example of how enzyme and transporter production can be made conditional on the presence of a nutrient to catabolize. | 2007 | 17786226 |
| a statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes. | among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. we investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution. | 2007 | 17877818 |
| environmental variability and modularity of bacterial metabolic networks. | biological systems are often modular: they can be decomposed into nearly-independent structural units that perform specific functions. the evolutionary origin of modularity is a subject of much current interest. recent theory suggests that modularity can be enhanced when the environment changes over time. however, this theory has not yet been tested using biological data. | 2007 | 17888177 |
| 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 |
| separating the effects of mutation and selection in producing dna skew in bacterial chromosomes. | many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. the relative contributions of selection and mutation in producing compositional skew are largely unknown. | 2007 | 17935620 |
| coupling genetics and proteomics to identify aphid proteins associated with vector-specific transmission of polerovirus (luteoviridae). | cereal yellow dwarf virus-rpv (cydv-rpv) is transmitted specifically by the aphids rhopalosiphum padi and schizaphis graminum in a circulative nonpropagative manner. the high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. studies of f(2) progeny from crosses of vector and nonvector genotypes of s. graminum showed that virus transmission efficiency ... | 2007 | 17959668 |
| coupling genetics and proteomics to identify aphid proteins associated with vector-specific transmission of polerovirus (luteoviridae). | cereal yellow dwarf virus-rpv (cydv-rpv) is transmitted specifically by the aphids rhopalosiphum padi and schizaphis graminum in a circulative nonpropagative manner. the high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. studies of f(2) progeny from crosses of vector and nonvector genotypes of s. graminum showed that virus transmission efficiency ... | 2007 | 17959668 |
| 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 |
| short-term temporal variability in airborne bacterial and fungal populations. | airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. as a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. cultivation-independent surveys of small-subunit rrna genes were conducted in order to identify the types ... | 2008 | 17981945 |
| short-term temporal variability in airborne bacterial and fungal populations. | airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. as a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. cultivation-independent surveys of small-subunit rrna genes were conducted in order to identify the types ... | 2008 | 17981945 |
| the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin. | the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i. | 2007 | 18021395 |
| genomic resources for myzus persicae: est sequencing, snp identification, and microarray design. | the green peach aphid, myzus persicae (sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. however, despite the significant damage inflicted by m. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. | 2007 | 18021414 |
| universal patterns of purifying selection at noncoding positions in bacteria. | to investigate the dependence of the number of regulatory sites per intergenic region on genome size, we developed a new method for detecting purifying selection at noncoding positions in clades of related bacterial genomes. we comprehensively quantified evidence of purifying selection at noncoding positions across bacteria and found several striking universal patterns. consistent with selection acting at transcriptional regulatory elements near the transcription start, we find a universal posit ... | 2008 | 18032729 |
| assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. | comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. | 2007 | 18047665 |
| parallel genomic evolution and metabolic interdependence in an ancient symbiosis. | obligate symbioses with nutrient-provisioning bacteria have originated often during animal evolution and have been key to the ecological diversification of many invertebrate groups. to date, genome sequences of insect nutritional symbionts have been restricted to a related cluster within gammaproteobacteria and have revealed distinctive features, including extreme reduction, rapid evolution, and biased nucleotide composition. using recently developed sequencing technologies, we show that sulcia ... | 2007 | 18048332 |
| symbiont-mediated protection. | despite the fact that all vertically transmitted symbionts sequester resources from their hosts and are therefore costly to maintain, there is an extraordinary diversity of them in invertebrates. some spread through host populations by providing their hosts with fitness benefits or by manipulating host sex ratio, but some do not: their maintenance in host lineages remains an enigma. in this review, i explore the evolutionary ecology of vertically transmitted symbionts and their impact on host re ... | 2007 | 18055391 |
| symbiont-mediated protection. | despite the fact that all vertically transmitted symbionts sequester resources from their hosts and are therefore costly to maintain, there is an extraordinary diversity of them in invertebrates. some spread through host populations by providing their hosts with fitness benefits or by manipulating host sex ratio, but some do not: their maintenance in host lineages remains an enigma. in this review, i explore the evolutionary ecology of vertically transmitted symbionts and their impact on host re ... | 2007 | 18055391 |
| impact of plant nutrients on the relationship between a herbivorous insect and its symbiotic bacteria. | the interactions between herbivorous insects and their symbiotic micro-organisms can be influenced by the plant species on which the insects are reared, but the underlying mechanisms are not understood. here, we identify plant nutrients, specifically amino acids, as a candidate factor affecting the impact of symbiotic bacteria on the performance of the phloem-feeding aphid aphis fabae. aphis fabae grew more slowly on the labiate plant lamium purpureum than on an alternative host plant vicia faba ... | 2008 | 18089538 |
| impact of plant nutrients on the relationship between a herbivorous insect and its symbiotic bacteria. | the interactions between herbivorous insects and their symbiotic micro-organisms can be influenced by the plant species on which the insects are reared, but the underlying mechanisms are not understood. here, we identify plant nutrients, specifically amino acids, as a candidate factor affecting the impact of symbiotic bacteria on the performance of the phloem-feeding aphid aphis fabae. aphis fabae grew more slowly on the labiate plant lamium purpureum than on an alternative host plant vicia faba ... | 2008 | 18089538 |
| the cyanobacterial endosymbiont of the unicellular algae rhopalodia gibba shows reductive genome evolution. | bacteria occur in facultative association and intracellular symbiosis with a diversity of eukaryotic hosts. recently, we have helped to characterise an intracellular nitrogen fixing bacterium, the so-called spheroid body, located within the diatom rhopalodia gibba. spheroid bodies are of cyanobacterial origin and exhibit features that suggest physiological adaptation to their intracellular life style. to investigate the genome modifications that have accompanied the process of endosymbiosis, her ... | 2008 | 18226230 |
| the rast server: rapid annotations using subsystems technology. | the number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. | 2008 | 18261238 |
| comparing patterns of natural selection across species using selective signatures. | comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. in the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and ... | 2008 | 18266472 |
| enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, nematostella vectensis, have microbial origins. | the shikimic acid pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. animals are considered to lack this pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino acids. we challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate pathway in an animal, the starlet sea anemone nematostella vectensis. molecular e ... | 2008 | 18268342 |
| high rate of mobilization for blactx-ms. | we constructed a phylogenetic analysis of class a beta-lactamases and found that the blactx-ms have been mobilized to plasmids approximately 10 times more frequently than other class a beta-lactamases. we also found that the blactx-ms are descended from a common ancestor that was incorporated in ancient times into the chromosome of the ancestor of kluyvera species through horizontal transfer. considerable sequence divergence has occurred among the descendents of that ancestral gene sequence sinc ... | 2008 | 18325257 |
| klebsiella pneumoniae multiresistance plasmid pmet1: similarity with the yersinia pestis plasmid pcry and integrative conjugative elements. | dissemination of antimicrobial resistance genes has become an important public health and biodefense threat. plasmids are important contributors to the rapid acquisition of antibiotic resistance by pathogenic bacteria. | 2008 | 18350140 |
| comparative genome analysis of "candidatus phytoplasma australiense" (subgroup tuf-australia i; rp-a) and "ca. phytoplasma asteris" strains oy-m and ay-wb. | the chromosome sequence of "candidatus phytoplasma australiense" (subgroup tuf-australia i; rp-a), associated with dieback in papaya, australian grapevine yellows in grapevine, and several other important plant diseases, was determined. the circular chromosome is represented by 879,324 nucleotides, a gc content of 27%, and 839 protein-coding genes. five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. potentia ... | 2008 | 18359806 |
| impact of transcription units rearrangement on the evolution of the regulatory network of gamma-proteobacteria. | in the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. however, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as e. coli among the prokaryotes. | 2008 | 18366643 |
| complete genome of the uncultured termite group 1 bacteria in a single host protist cell. | termites harbor a symbiotic gut microbial community that is responsible for their ability to thrive on recalcitrant plant matter. the community comprises diverse microorganisms, most of which are as yet uncultivable; the detailed symbiotic mechanism remains unclear. here, we present the first complete genome sequence of a termite gut symbiont-an uncultured bacterium named rs-d17 belonging to the candidate phylum termite group 1 (tg1). tg1 is a dominant group in termite guts, found as intracellul ... | 2008 | 18391199 |
| reducing the false positive rate in the non-parametric analysis of molecular coevolution. | the strength of selective constraints operating on amino acid sites of proteins has a multifactorial nature. in fact, amino acid sites within proteins coevolve due to their functional and/or structural relationships. different methods have been developed that attempt to account for the evolutionary dependencies between amino acid sites. researchers have invested a significant effort to increase the sensitivity of such methods. however, the difficulty in disentangling functional co-dependencies f ... | 2008 | 18402697 |
| investigations of oligonucleotide usage variance within and between prokaryotes. | oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), dna base-stacking energy (dinucleotides), and dna structural conformation (di- to tetranucleotides). we wanted to assess the statistical information potential of different dna 'word-sizes' and explore how oligonucleotide frequencies differ in coding and non-coding regions. in addition, we used oligonucleotide frequencies to investigate dna composition and how d ... | 2008 | 18421372 |
| gene prediction in metagenomic fragments: a large scale machine learning approach. | metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. the amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. in contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous seq ... | 2008 | 18442389 |
| extreme polyploidy in a large bacterium. | cells rely on diffusion to move metabolites and biomolecules. diffusion is highly efficient but only over short distances. although eukaryotic cells have broken free of diffusion-dictated constraints on cell size, most bacteria and archaea are forced to remain small. exceptions to this rule are found among the bacterial symbionts of surgeonfish; epulopiscium spp. are cigar-shaped cells that reach lengths in excess of 600 mum. a large epulopiscium contains thousands of times more dna than a bacte ... | 2008 | 18445653 |
| ogtree: a tool for creating genome trees of prokaryotes based on overlapping genes. | ogtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. the overlapping genes (ogs) are defined as adjacent genes whose coding sequences overlap partially or entirely. in fact, ogs are ubiquitous in microbial genomes and more conserved between species than non-ogs. based on these properties, it has been suggested that ogs can serve as better phylogenetic characters ... | 2008 | 18456706 |
| infection dynamics of coexisting beta- and gammaproteobacteria in the nested endosymbiotic system of mealybugs. | we investigated the infection dynamics of endosymbiotic bacteria in the developmental course of the mealybugs planococcus kraunhiae and pseudococcus comstocki. molecular phylogenetic analyses identified a betaproteobacterium and a gammaproteobacterium from each of the mealybug species. the former bacterium was related to the beta-endosymbionts of other mealybugs, i.e., "candidatus tremblaya princeps," and formed a compact clade in the betaproteobacteria. meanwhile, the latter bacterium was relat ... | 2008 | 18469124 |
| triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. | bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. this difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. | 2008 | 18471287 |
| interactions of chaperonin with a weakly active anthranilate synthase from the aphid endosymbiont buchnera aphidicola. | the endosymbiotic bacterium buchnera provides its aphid host with essential amino acids. buchnera is typical of intracellular symbiotic and parasitic microorganisms in having a small effective population size, which is believed to accelerate genetic drift and reduce the stability of gene products. it is hypothesized that buchnera mitigates protein instability with an increased production of the chaperonins groesl. in this paper, we report the expression and functional analysis of trpe, a plasmid ... | 2008 | 18478288 |
| evolution of the secondary symbiont "candidatus serratia symbiotica" in aphid species of the subfamily lachninae. | buchnera aphidicola bcc, the primary endosymbiont of the aphid cinara cedri (subfamily lachninae), is losing its symbiotic capacity and might be replaced by the coresident "candidatus serratia symbiotica." phylogenetic and morphological analyses within the subfamily lachninae indicate two different "ca. serratia symbiotica" lineages and support the longtime coevolution of both symbionts in c. cedri. | 2008 | 18502932 |
| ests from the microsporidian edhazardia aedis. | microsporidia are a group of parasites related to fungi that infect a wide variety of animals and have gained recognition from the medical community in the past 20 years due to their ability to infect immuno-compromised humans. microsporidian genomes range in size from 2.3 to 19.5 mbp, but almost all of our knowledge comes from species that have small genomes (primarily from the human parasite encephalitozoon cuniculi and the locust parasite antonospora locustae). we have conducted an est survey ... | 2008 | 18570666 |
| aphids. | 2008 | 18579086 | |
| the striking case of tryptophan provision in the cedar aphid cinara cedri. | buchnera aphidicola bcc has lost its symbiotic role as the tryptophan supplier to the aphid cinara cedri. we report the presence of a plasmid in this endosymbiont that contains the trpeg genes. the remaining genes for the pathway (trpdcba) are located on the chromosome of the secondary endosymbiont "candidatus serratia symbiotica." thus, we propose that a symbiotic consortium is necessary to provide tryptophan. | 2008 | 18586942 |
| toxic introns and parasitic intein in coxiella burnetii: legacies of a promiscuous past. | the genome of the obligate intracellular pathogen coxiella burnetii contains a large number of selfish genetic elements, including two group i introns (cbu.l1917 and cbu.l1951) and an intervening sequence that interrupts the 23s rrna gene, an intein (cbu.dnab) within dnab and 29 insertion sequences. here, we describe the ability of the intron-encoded rnas (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of cbu.dnab. when expressed in e ... | 2008 | 18606739 |
| borrelia burgdorferi vlse antigenic variation is not mediated by reca. | reca is a key protein linking genetic recombination to dna replication and repair in bacteria. previous functional characterization of borrelia burgdorferi reca indicated that the protein is mainly involved in genetic recombination rather than dna repair. genetic recombination may play a role in b. burgdorferi persistence by generation of antigenic variation. we report here the isolation of a reca null mutant in an infectious b. burgdorferi strain. comparison of the in vitro growth characteristi ... | 2008 | 18606826 |
| tuberculosis vaccine strain mycobacterium bovis bcg russia is a natural reca mutant. | the current tuberculosis vaccine is a live vaccine derived from mycobacterium bovis and attenuated by serial in vitro passaging. all vaccine substrains in use stem from one source, strain bacille calmette-guérin. however, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. | 2008 | 18637199 |
| an insecticidal groel protein with chitin binding activity from xenorhabdus nematophila. | xenorhabdus nematophila secretes insecticidal proteins to kill its larval prey. we have isolated an approximately 58-kda groel homolog, secreted in the culture medium through outer membrane vesicles. the protein was orally insecticidal to the major crop pest helicoverpa armigera with an lc50 of approximately 3.6 microg/g diet. for optimal insecticidal activity all three domains of the protein, apical, intermediate, and equatorial, were necessary. the apical domain alone was able to bind to the l ... | 2008 | 18667427 |
| complete rpob gene sequencing as a suitable supplement to dna-dna hybridization for bacterial species and genus delineation. | dna-dna hybridization (ddh), the gold standard for bacterial species delineation, is a laborious method and the alternative, average nucleotide identity (ani), a genomic sequence-derived parameter, is not applicable to non-sequenced species. a universal cut-off value to delineate bacterial species does not exist, yet a ddh value <70 % and ani <95+/-0.5 % have proved useful in selected examples. we herein compare published values for ddh and ani with sequence similarity of rpob gene sequences ret ... | 2008 | 18676461 |
| the obligate mutualist wigglesworthia glossinidia influences reproduction, digestion, and immunity processes of its host, the tsetse fly. | tsetse flies (diptera: glossinidae) are vectors for trypanosome parasites, the agents of the deadly sleeping sickness disease in africa. tsetse also harbor two maternally transmitted enteric mutualist endosymbionts: the primary intracellular obligate wigglesworthia glossinidia and the secondary commensal sodalis glossinidius. both endosymbionts are transmitted to the intrauterine progeny through the milk gland secretions of the viviparous female. we administered various antibiotics either contin ... | 2008 | 18689507 |
| the insecticidal activity of recombinant garlic lectins towards aphids. | the heterodimeric and homodimeric garlic lectins asai and asaii were produced as recombinant proteins in the yeast pichia pastoris. the proteins were purified as functional dimeric lectins, but underwent post-translational proteolysis. recombinant asaii was a single homogenous polypeptide which had undergone c-terminal processing similar to that occurring in planta. the recombinant asai was glycosylated and subject to variable and heterogenous proteolysis. both lectins showed insecticidal effect ... | 2008 | 18707000 |
| complex chloroplast rna metabolism: just debugging the genetic programme? | the gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. this gain in complexity affects in particular rna metabolism, specifically the transcription and maturation of rna. mature chloroplast rna is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional rna polymerases and sigma factors, and sequence-specific rna maturation factors promoting rna splicing, editing, end formation an ... | 2008 | 18755031 |
| comparative phylogenomics and multi-gene cluster analyses of the citrus huanglongbing (hlb)-associated bacterium candidatus liberibacter. | huanglongbing (hlb, previously known as citrus greening), is associated with candidatus liberibacter species and is a serious threat to citrus production world-wide. the pathogen is a gram negative, unculturable, phloem-limited bacterium with limited known genomic information. expanding the genetic knowledge of this organism may provide better understanding of the pathogen and possibly develop effective strategies for control and management of hlb. | 2008 | 18755041 |
| fine-scale cospeciation between brachycaudus and buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids. | aphids harbour an obligatory symbiont, buchnera aphidicola, providing essential amino acids not supplied by their diet. these bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. we investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus brachycaudus. we used dna-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and buchnera species and to infer asso ... | 2009 | 18782748 |
| fine-scale cospeciation between brachycaudus and buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids. | aphids harbour an obligatory symbiont, buchnera aphidicola, providing essential amino acids not supplied by their diet. these bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. we investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus brachycaudus. we used dna-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and buchnera species and to infer asso ... | 2009 | 18782748 |
| large-scale reconstruction and phylogenetic analysis of metabolic environments. | the topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. here we introduce the concept of a metabolic network's "seed set"--the set of compounds that, based on the network topology, are exogenously acquired--and provide a methodological framework to computationally infer the seed set of a given network. such seed sets form ecological "interfaces" between metabolic networks and their surrou ... | 2008 | 18787117 |
| endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(a) tracts. | among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160-790 kb) and most a + t-rich (>70%) bacterial genomes known to date. these genomes are riddled with poly(a) tracts, and 5-50% of genes contain tracts of 10 as or more. here, we demonstrate transcriptional slippage at poly(a) tracts within genes of buchnera aphidicola associated with aphids and blochmannia pennsylvanicus associated with ants. se ... | 2008 | 18815381 |
| suppression of deltabipa phenotypes in escherichia coli by abolishment of pseudouridylation at specific sites on the 23s rrna. | the bipa protein of escherichia coli has intriguing similarities to the elongation factor subfamily of gtpases, including ef-tu, ef-g, and lepa. in addition, phenotypes of a bipa deletion mutant suggest that bipa is involved in regulation of a variety of pathways. these two points have led to speculation that bipa may be a novel regulatory protein that affects efficient translation of target genes through direct interaction with the ribosome. we isolated and characterized suppressors of the cold ... | 2008 | 18820021 |
| unassigned murf1 of kinetoplastids codes for nadh dehydrogenase subunit 2. | in a previous study, we conducted a large-scale similarity-free function prediction of mitochondrion-encoded hypothetical proteins, by which the hypothetical gene murf1 (maxicircle unidentified reading frame 1) was assigned as nad2, encoding subunit 2 of nadh dehydrogenase (complex i of the respiratory chain). this hypothetical gene occurs in the mitochondrial genome of kinetoplastids, a group of unicellular eukaryotes including the causative agents of african sleeping sickness and leishmaniasis ... | 2008 | 18831753 |
| bioinformatics identification of murj (mvin) as the peptidoglycan lipid ii flippase in escherichia coli. | peptidoglycan is a cell-wall glycopeptide polymer that protects bacteria from osmotic lysis. whereas in gram-positive bacteria it also serves as scaffold for many virulence factors, in gram-negative bacteria, peptidoglycan is an anchor for the outer membrane. for years, we have known the enzymes required for the biosynthesis of peptidoglycan; what was missing was the flippase that translocates the lipid-anchored precursors across the cytoplasmic membrane before their polymerization into mature p ... | 2008 | 18832143 |
| accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria. | despite a large agreement between ribosomal rna and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. for instance, the position of the hyperthermophilic aquificales is debated, as their commonly observed position close to thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. indeed, another view, based on the analysis of rare genomic c ... | 2008 | 18834516 |
| metasim: a sequencing simulator for genomics and metagenomics. | the new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. there is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. | 2008 | 18841204 |
| preferred and avoided codon pairs in three domains of life. | alternative synonymous codons are not used with equal frequencies. in addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. the codon context can influence both translational accuracy and elongation rates. however, it is not known how strong or conserved the codon context preferences in different organisms are. we analyzed 138 organisms (bacteria, archaea and eukaryotes) to find conserved patterns of codon pairs. | 2008 | 18842120 |
| metageneannotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. | recent advances in dna sequencers are accelerating genome sequencing, especially in microbes, and complete and draft genomes from various species have been sequenced in rapid succession. here, we present a comprehensive gene prediction tool, the metageneannotator (mga), which precisely predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths. the mga integrates statistical models of prophage genes, in addition to those of bacterial ... | 2008 | 18940874 |
| chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race. | the genomes of pathogens are thought to have evolved under selective pressure provided by the host in a coevolutionary arms race (the 'red queen's hypothesis'). traditionally, adaptation by pathogens is thought to rely not on whole chromosome dynamics but on gain/loss of specific genes, yielding differential abilities to infect distinct tissues. thus, it is not known whether distinct host organs differently shape the genome of the same pathogen. we tested this hypothesis using chlamydia trachoma ... | 2008 | 18947394 |
| using mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. | plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. to understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. since extensive data support the proposal that foreign dna acquires the host's nucleotide composition during long-term residence, comparison of nucleotide ... | 2008 | 18953039 |
| a genomic distance based on mum indicates discontinuity between most bacterial species and genera. | the fundamental unit of biological diversity is the species. however, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ani), which detects the dna conservation of the core genome, and the dna content, which calculates the proportion of dna share ... | 2009 | 18978054 |
| a genomic distance based on mum indicates discontinuity between most bacterial species and genera. | the fundamental unit of biological diversity is the species. however, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ani), which detects the dna conservation of the core genome, and the dna content, which calculates the proportion of dna share ... | 2009 | 18978054 |
| whole-genome mutational biases in bacteria. | a fundamental biological question is what forces shape the guanine plus cytosine (gc) content of genomes. we studied the specificity and rate of different mutational biases in real time in the bacterium salmonella typhimurium under conditions of strongly reduced selection and in the absence of the major dna repair systems involved in repairing common spontaneous mutations caused by oxidized and deaminated dna bases. the mutational spectrum was determined by whole-genome sequencing of two s. typh ... | 2008 | 19001264 |
| mosaic: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. | the recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. it is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. | 2008 | 19038022 |
| network-based approaches for linking metabolism with environment. | progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat. | 2008 | 19040774 |
| the dynamic genetic repertoire of microbial communities. | community genomic data have revealed multiple levels of variation between and within microbial consortia. this variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. in the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. a major unresolved question is how much of the observed variation is due to neutral vs. adaptive processe ... | 2008 | 19054116 |
| the dynamic genetic repertoire of microbial communities. | community genomic data have revealed multiple levels of variation between and within microbial consortia. this variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. in the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. a major unresolved question is how much of the observed variation is due to neutral vs. adaptive processe ... | 2008 | 19054116 |
| comparative genomics of vesicomyid clam (bivalvia: mollusca) chemosynthetic symbionts. | the vesicomyidae (bivalvia: mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. they exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible. | 2008 | 19055818 |
| selection for translational robustness in buchnera aphidicola, endosymbiotic bacteria of aphids. | its strong intergenerational bottlenecks and effectively asexual reproduction have led buchnera aphidicola, the endocellular symbiotic bacterium of aphids, to spectacular evolutionary and genomic changes in comparison with its free-living bacterial cousins. these changes summarize into high fixation rates of mildly deleterious destabilizing mutations. this predicts a sharp decline of its fitness and the consequent early demise of this endosymbiotic bacterium. its survival for hundreds of million ... | 2009 | 19126868 |
| symbiotic bacteria enable insect to use a nutritionally inadequate diet. | animals generally require a dietary supply of various nutrients (vitamins, essential amino acids, etc.) because their biosynthetic capabilities are limited. the capacity of aphids to use plant phloem sap, with low essential amino acid content, has been attributed to their symbiotic bacteria, buchnera aphidicola, which can synthesize these nutrients; but this has not been demonstrated empirically. we demonstrate here that phloem sap obtained from the severed stylets of pea aphids acyrthosiphon pi ... | 2009 | 19129128 |
| symbiotic bacteria enable insect to use a nutritionally inadequate diet. | animals generally require a dietary supply of various nutrients (vitamins, essential amino acids, etc.) because their biosynthetic capabilities are limited. the capacity of aphids to use plant phloem sap, with low essential amino acid content, has been attributed to their symbiotic bacteria, buchnera aphidicola, which can synthesize these nutrients; but this has not been demonstrated empirically. we demonstrate here that phloem sap obtained from the severed stylets of pea aphids acyrthosiphon pi ... | 2009 | 19129128 |
| host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs. | host-symbiont co-speciation and reductive genome evolution have been commonly observed among obligate endocellular insect symbionts, while such examples have rarely been identified among extracellular ones, the only case reported being from gut symbiotic bacteria of stinkbugs of the family plataspidae. considering that gut symbiotic communities are vulnerable to invasion of foreign microbes, gut symbiotic associations have been thought to be evolutionarily not stable. stinkbugs of the family aca ... | 2009 | 19146674 |
| the dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. | among cellular organisms, symbiotic bacteria provide the extreme examples of genome degradation and reduction. however, only isolated snapshots of eroding symbiont genomes have previously been available. we documented the dynamics of symbiont genome evolution by sequencing seven strains of buchnera aphidicola from pea aphid hosts. we estimated a spontaneous mutation rate of at least 4 x 10(-9) substitutions per site per replication, which is more than 10 times as high as the rates previously est ... | 2009 | 19150844 |
| minimum contradiction matrices in whole genome phylogenies. | minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ... | 2008 | 19204821 |
| comphy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets. | with the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. we developed a new tool comphy, 'composite distance phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny. | 2009 | 19208152 |
| codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in lawsonia intracellularis. | in this study, the factors driving genome-wide patterns of codon usages in lawsonia intracellularis genome are determined. for genes on the chromosome of the bacterium, it is found that the most important source of variation results from strand-specific mutational biases. a lesser trend of variation is attributable to genes that are presumed as horizontally transferred. these putative alien genes are unusually gc richer than the other genes, whereas horizontally transferred genes have been obser ... | 2009 | 19221094 |
| a fragile metabolic network adapted for cooperation in the symbiotic bacterium buchnera aphidicola. | in silico analyses provide valuable insight into the biology of obligately intracellular pathogens and symbionts with small genomes. there is a particular opportunity to apply systems-level tools developed for the model bacterium escherichia coli to study the evolution and function of symbiotic bacteria which are metabolically specialised to overproduce specific nutrients for their host and, remarkably, have a gene complement that is a subset of the e. coli genome. | 2009 | 19232131 |
| genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. | the family rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. within this family, many rhizobium and sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as agrobacterium are plant pathogens. these contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. members of the rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, ... | 2009 | 19251847 |
| structure and biological function of the rna pyrophosphohydrolase bdrpph from bdellovibrio bacteriovorus. | until recently, the mechanism of mrna decay in bacteria was thought to be different from that of eukaryotes. this paradigm changed with the discovery that rpph (orf176/nudh/ygdp), an escherichia coli enzyme that belongs to the nudix superfamily, is an rna pyrophosphohydrolase that initiates mrna decay by cleaving pyrophosphate from the 5'-triphosphate. here we report the 1.9 angstroms resolution structure of the nudix hydrolase bdrpph from bdellovibrio bacteriovorus, a bacterium that feeds on ot ... | 2009 | 19278661 |
| aphids acquired symbiotic genes via lateral gene transfer. | aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist buchnera aphidicola (gamma-proteobacteria). buchnera has lost many of the genes that appear to be essential for bacterial life. from the bacteriocyte of the pea aphid acyrthosiphon pisum, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. southern blot analysis demonstrated that they are encoded in the aphid genome. in this stu ... | 2009 | 19284544 |