| recent functional insights into the role of (p)ppgpp in bacterial physiology. | the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ... | 2015 | 25853779 |
| 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 |
| vesiculation from pseudomonas aeruginosa under sos. | bacterial infections can be aggravated by antibiotic treatment that induces sos response and vesiculation. this leads to a hypothesis concerning association of sos with vesiculation. to test it, we conducted multiple analyses of outer membrane vesicles (omvs) produced from the pseudomonas aeruginosa wild type in which sos is induced by ciprofloxacin and from the lexa noncleavable (lexan) strain in which sos is repressed. the levels of omv proteins, lipids, and cytotoxicity increased for both the ... | 2012 | 22448133 |
| identification and characterization of phytoplasmal genes, employing a novel method of isolating phytoplasmal genomic dna. | phytoplasmas are unculturable, insect-transmissible plant pathogens belonging to the class mollicutes. to be transmitted, the phytoplasmas replicate in the insect body and are delivered to the insect's salivary glands, from where they are injected into the recipient plant. because phytoplasmas cannot be cultured, any attempt to recover phytoplasmal dna from infected plants or insects has resulted in preparations with a large background of host dna. thus, studies of the phytoplasmal genome have b ... | 2003 | 14594823 |
| 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 |
| across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage. | the gc content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic gc content are observed within many bacterial phyla, including both gram negative and gram positive phyla. thus, divergent genomic gc content has evolved repeatedly in widely separated bacterial taxa. since genomic gc content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic gc content within eight different phyla or classes of bacteria. w ... | 2011 | 21423704 |
| srpdb (signal recognition particle database). | signal recognition particle (srp) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. the srp database (srpdb) provides compilations of srp components, ordered alphabetically and phylogenetically. alignments emphasize phylogenetically-supported base pairs in srp rna and conserved residues in the proteins. data are provided in various formats including a column arrangement for improved access and simplified computati ... | 2001 | 11125080 |
| 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 |
| 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 |
| whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution. | we present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (ffps) of whole proteomes. features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. the selection of feature length is critical in the ffp method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. our ffp trees are constructe ... | 2009 | 20018669 |
| whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution. | we present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (ffps) of whole proteomes. features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. the selection of feature length is critical in the ffp method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. our ffp trees are constructe ... | 2009 | 20018669 |
| assessing the quality of whole genome alignments in bacteria. | comparing genomes is an essential preliminary step to solve many problems in biology. matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. the first measure is based o ... | 2009 | 20049164 |
| evolutionary pressures on simple sequence repeats in prokaryotic coding regions. | simple sequence repeats (ssrs) are indel mutational hotspots in genomes. in prokaryotes, ssr loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. by analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of ssrs in coding regions. we demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are m ... | 2011 | 22123746 |
| evolutionary pressures on simple sequence repeats in prokaryotic coding regions. | simple sequence repeats (ssrs) are indel mutational hotspots in genomes. in prokaryotes, ssr loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. by analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of ssrs in coding regions. we demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are m ... | 2011 | 22123746 |
| xenobiotic efflux in bacteria and fungi: a genomics update. | | 2011 | 21692371 |
| insights from genomic comparisons of genetically monomorphic bacterial pathogens. | some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. it has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. the genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. some ... | 2012 | 22312053 |
| dna replication and strand asymmetry in prokaryotic and mitochondrial genomes. | different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. here i summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endos ... | 2012 | 22942672 |
| short and long-term genome stability analysis of prokaryotic genomes. | gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. there is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on ... | 2013 | 23651581 |
| reconstruction of phyletic trees by global alignment of multiple metabolic networks. | in the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. in contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. | 2013 | 23368411 |
| the genome of the intracellular bacterium of the coastal bivalve, solemya velum: a blueprint for thriving in and out of symbiosis. | symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. these associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of ch ... | 2014 | 25342549 |
| systems biology perspectives on minimal and simpler cells. | the concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. this broad concept encompasses extreme reductions of genomes, the last universal common ancestor (luca), the creation of semiartificial cells, and the design of protocells and chassis cells. here we review these different areas of research and identify common and complementary aspects of each one. we focus on systems biology, a discipline that is greatly facilitating the c ... | 2014 | 25184563 |
| requirement of the flagellar protein export apparatus component flio for optimal expression of flagellar genes in helicobacter pylori. | flagellar biogenesis in helicobacter pylori involves the coordinated expression of flagellar genes with assembly of the flagellum. the h. pylori flagellar genes are organized into three regulons based on the sigma factor needed for their transcription (rpod [σ(80)], rpon [σ(54)], or flia [σ(28)]). transcription of rpon-dependent genes is activated by a two-component system consisting of the sensor kinase flgs and the response regulator flgr. while the cellular cues sensed by the flgs/flgr two-co ... | 2014 | 24837287 |
| identification of the main venom protein components of aphidius ervi, a parasitoid wasp of the aphid model acyrthosiphon pisum. | endoparasitoid wasps are important natural enemies of the widely distributed aphid pests and are mainly used as biological control agents. however, despite the increased interest on aphid interaction networks, only sparse information is available on the factors used by parasitoids to modulate the aphid physiology. our aim was here to identify the major protein components of the venom injected at oviposition by aphidius ervi to ensure successful development in its aphid host, acyrthosiphon pisum. | 2014 | 24884493 |
| the bacterial pangenome as a new tool for analysing pathogenic bacteria. | the bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. in this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. we have also shown that the pangenome may be used as a new tool ... | 2015 | 26442149 |
| bacterial antisense rnas are mainly the product of transcriptional noise. | cis-encoded antisense rnas (asrnas) are widespread along bacterial transcriptomes. however, the role of most of these rnas remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. we show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asrnas is exponentially dependent on the genomic at content and that expression of asrna at low levels exerts little impact in terms of energy c ... | 2016 | 26973873 |
| metagenomics: application of genomics to uncultured microorganisms. | metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of dna from an assemblage of microorganisms. the development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. this evidence was derived from analyses of 16s rrna gene sequences amplified directly from the environment, an approach that avo ... | 2004 | 15590779 |
| global analysis of predicted proteomes: functional adaptation of physical properties. | the physical characteristics of proteins are fundamentally important in organismal function. we used the complete predicted proteomes of >100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. theoretical 2d gels were constructed with axes of protein mass and charge (pi) and converted to density estimates comparable across all types and sizes of proteome. we asked whether we could detect general patterns of proteome conservation and va ... | 2004 | 15150418 |
| 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 |
| 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 |
| a system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature. | a broadly accepted and stable biological classification system is a prerequisite for biological sciences. it provides the means to describe and communicate about life without ambiguity. current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. the current system is thus inadequate to classify and name the immense genetic diversity within s ... | 2014 | 24586551 |
| beyond society: the evolution of organismality. | the evolution of organismality is a social process. all organisms originated from groups of simpler units that now show high cooperation among the parts and are nearly free of conflicts. we suggest that this near-unanimous cooperation be taken as the defining trait of organisms. consistency then requires that we accept some unconventional organisms, including some social insect colonies, some microbial groups and viruses, a few sexual partnerships and a number of mutualistic associations. whethe ... | 2009 | 19805423 |
| working together for the common good: cell-cell communication in bacteria. | the 4th asm conference on cell-cell communication in bacteria was held in miami, fl, from 6 to 9 november 2011. this review highlights three key themes that emerged from the many exciting talks and poster presentations in the area of quorum sensing: sociomicrobiology, signal transduction mechanisms, and interspecies communication. | 2012 | 22389476 |
| bacterial endosymbiosis in a chordate host: long-term co-evolution and conservation of secondary metabolism. | intracellular symbiosis is known to be widespread in insects, but there are few described examples in other types of host. these symbionts carry out useful activities such as synthesizing nutrients and conferring resistance against adverse events such as parasitism. such symbionts persist through host speciation events, being passed down through vertical transmission. due to various evolutionary forces, symbionts go through a process of genome reduction, eventually resulting in tiny genomes wher ... | 2013 | 24324632 |
| molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix. | tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ... | 2014 | 25108393 |
| 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 |
| genome degeneration affects both extracellular and intracellular bacterial endosymbionts. | the obligate intracellular bacterial endosymbionts of insects are a paradigm for reductive genome evolution. a study published recently in bmc biology demonstrates that similar evolutionary forces shaping genome structure may also apply to extracellular endosymbionts. | 2009 | 19435469 |
| read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies. | there are a growing number of next-generation sequencing technologies. at present, the most cost-effective options also produce the shortest reads. however, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. this reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. | 2010 | 20634954 |
| characterization of species-specific repeats in 613 prokaryotic species. | prokaryotes are in general believed to possess small, compactly organized genomes, with repetitive sequences forming only a small part of them. nonetheless, many prokaryotic genomes in fact contain species-specific repeats (>85 bp long genomic sequences with less than 60% identity to other species) as we have previously demonstrated. however, it is not known at present how frequent such species-specific repeats are and what their functional roles in bacterial genomes may be. therefore, we have c ... | 2012 | 22368180 |
| winding paths to simplicity: genome evolution in facultative insect symbionts. | symbiosis between organisms is an important driving force in evolution. among the diverse relationships described, extensive progress has been made in insect-bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. to bridge the gap between those obligate symbionts with extremely reduced genomes ... | 2016 | 27519426 |
| protein targeting to the bacterial cytoplasmic membrane. | proteins that perform their activity within the cytoplasmic membrane or outside this cell boundary must be targeted to the translocation site prior to their insertion and/or translocation. in bacteria, several targeting routes are known; the secb- and the signal recognition particle-dependent pathways are the best characterized. recently, evidence for the existence of a third major route, the twin-arg pathway, was gathered. proteins that use either one of these three different pathways possess s ... | 1999 | 10066835 |
| terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. | rapid analysis of microbial communities has proven to be a difficult task. this is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16s rrna comparative sequence analysis. we describe a web-based research tool located at the ribosomal database project web site (http://www.cme.msu.ed ... | 2000 | 10919828 |
| genetic conflict and conditional altruism in social aphid colonies. | although kin selection is central to the modern study of social evolution, recent studies of social species have revealed that no simple relationship exists between levels of kinship and sociality. the soldier-producing aphids are unique among highly social animals because, barring movement by aphids between colonies, they occur in clonal groups of genetically identical individuals. potentially, clonality simplifies efforts to understand social evolution in aphids by obviating issues of intragro ... | 2001 | 11562469 |
| bacterial menageries inside insects. | | 2001 | 11171951 |
| endosymbiotic bacteria in the esophageal organ of glossiphoniid leeches. | we characterized the intracellular symbiotic bacteria of the hematophagous glossiphoniid leeches placobdelloides siamensis and a parabdella sp. these leeches have a specialized structure called an "esophageal organ," the cells of which harbor bacterial symbionts. from the esophageal organ of each species, a 1.5-kb eubacterial 16s rrna gene segment was amplified by pcr, cloned, and sequenced. diagnostic pcr detected the symbiont in the esophageal organ and intestine. phylogenetic analysis of the ... | 2002 | 12200323 |
| abstracts from the xiii international entomophagous insects workshop, july 27-31, 2003, tucson, arizona, usa. | | 2003 | 16292358 |
| from gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. | the rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. however, extensive lateral gene transfer (lgt) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. the group for which cases of lgt are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-proteobacteria, an ... | 2003 | 12975657 |
| coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam calyptogena magnifica. | the hydrothermal vent clam calyptogena magnifica (bivalvia: vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. this symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. if symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if ... | 2003 | 12676683 |
| determination of the core of a minimal bacterial gene set. | the availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. the availabl ... | 2004 | 15353568 |
| proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison. | we propose a new method for classifying and identifying transmembrane (tm) protein functions in proteome-scale by applying a single-linkage clustering method based on tm topology similarity, which is calculated simply from comparing the lengths of loop regions. in this study, we focused on 87 prokaryotic tm proteomes consisting of 31 proteobacteria, 22 gram-positive bacteria, 19 other bacteria, and 15 archaea. prior to performing the clustering, we first categorized individual tm protein sequenc ... | 2004 | 15273311 |
| predicting transmembrane beta-barrels in proteomes. | very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. one reason is that only very few high-resolution structures for transmembrane beta-barrel (tmb) proteins have been determined thus far. here we introduced the design, statistics and results of a novel profile-based hidden markov model for the prediction and discrimination of tmbs. the method carefully attempts to avoid over-fitting the sparse experimental data. while our model training and sc ... | 2004 | 15141026 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| branchclust: a phylogenetic algorithm for selecting gene families. | automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. the first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is ofte ... | 2007 | 17425803 |
| the power of phylogenetic approaches to detect horizontally transferred genes. | horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. high genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? the answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred ge ... | 2007 | 17376230 |
| a global gene evolution analysis on vibrionaceae family using phylogenetic profile. | vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. in this work we propose an improved phylogenetic profile analysis on 14 vibrionaceae genomes, to study the evolution of this family on the basis of gene content. the phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently p ... | 2007 | 17430568 |
| purifying selection in mitochondria, free-living and obligate intracellular proteobacteria. | the effectiveness of elimination of slightly deleterious mutations depends mainly on drift and recombination frequency. here we analyze the influence of these two factors on the strength of the purifying selection in mitochondrial and proteobacterial orthologous genes taking into account the differences in the organism lifestyles. | 2007 | 17295908 |
| phylogenetic signal and functional categories in proteobacteria genomes. | a comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. in this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods. | 2007 | 17288580 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| aphids. | | 2008 | 18579086 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. | driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. while the use of in silico models is still in its early stages for del ... | 2009 | 19946878 |
| windshield splatter analysis with the galaxy metagenomic pipeline. | how many species inhabit our immediate surroundings? a straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. the windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. unfortunately the analysis of biological material collected in that manner, as with most metagenomic studies, proves to be rather demanding due to the large number ... | 2009 | 19819906 |
| stratification of co-evolving genomic groups using ranked phylogenetic profiles. | previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. the evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. herein, we present rank-blast, a novel approach ... | 2009 | 19860884 |