| new insights on the evolutionary history of aphids and their primary endosymbiont buchnera aphidicola. | since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont, buchnera aphidicola, insects and bacteria have coevolved. due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. here we report, based on data from b. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symb ... | 2011 | 21350635 |
| genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont. | the symbiosis of the pea aphid acyrthosphion pisum with the bacterium buchnera aphidicola aps represents the best-studied insect obligate symbiosis. here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. in doing so, we address four issues central to understanding the patterns and processes operating at the a. pisum/buchnera aps interface. these four issue ... | 2011 | 21390549 |
| genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis. | the pervasive influence of resident microorganisms on the phenotype of their hosts is exemplified by the intracellular bacterium buchnera aphidicola, which provides its aphid partner with essential amino acids (eaas). we investigated variation in the dietary requirement for eaas among four pea aphid (acyrthosiphon pisum) clones. buchnera-derived nitrogen contributed to the synthesis of all eaas for which aphid clones required a dietary supply, and to none of the eaas for which all four clones ha ... | 2011 | 21392141 |
| large-scale label-free quantitative proteomics of the pea aphid-buchnera symbiosis. | many insects are nutritionally dependent on symbiotic microorganisms that have tiny genomes and are housed in specialized host cells called bacteriocytes. the obligate symbiosis between the pea aphid acyrthosiphon pisum and the ?-proteobacterium buchnera aphidicola (only 584 predicted proteins) is particularly amenable for molecular analysis because the genomes of both partners have been sequenced. to better define the symbiotic relationship between this aphid and buchnera, we used large-scale, ... | 2011 | 21421797 |
| diversity of bacterial type ii toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. | type ii toxin-antitoxin (ta) systems are generally composed of two genes organized in an operon, encoding a labile antitoxin and a stable toxin. they were first discovered on plasmids where they contribute to plasmid stability by a phenomenon denoted as 'addiction', and subsequently in bacterial chromosomes. to discover novel families of antitoxins and toxins, we developed a bioinformatics approach based on the 'guilt by association' principle. extensive experimental validation in escherichia co ... | 2011 | 21422074 |
| phylogenetic distribution and evolutionary history of bacterial dead-box proteins. | dead-box proteins are found in all domains of life and participate in almost all cellular processes that involve rna. the presence of dead and helicase_c conserved domains distinguish these proteins. dead-box proteins exhibit rna-dependent atpase activity in vitro, and several also show rna helicase activity. in this study, we analyzed the distribution and architecture of dead-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. we i ... | 2011 | 21437710 |
| metabolic modeling of endosymbiont genome reduction on a temporal scale. | a fundamental challenge in systems biology is whether a cell-scale metabolic model can predict patterns of genome evolution by realistically accounting for associated biochemical constraints. here, we study the order in which genes are lost in an in silico evolutionary process, leading from the metabolic network of escherichia coli to that of the endosymbiont buchnera aphidicola. we examine how this order correlates with the order by which the genes were actually lost, as estimated from a phylog ... | 2011 | 21451589 |
| bacterioneuston community structure in the southern baltic sea and its dependence on meteorological conditions. | the bacterial community in the sea surface microlayer (sml) (bacterioneuston) is exposed to unique physicochemical properties and stronger meteorological influences than the bacterial community in the underlying water (ulw) (bacterioplankton). despite extensive research, however, the structuring factors of the bacterioneuston remain enigmatic. the aim of this study was to examine the effect of meteorological conditions on bacterioneuston and bacterioplankton community structures and to identify ... | 2011 | 21478321 |
| symbiont infection affects aphid defensive behaviours. | aphids harbour both an obligate bacterial symbiont, buchnera aphidicola, and a wide range of facultative ones. facultative symbionts can modify morphological, developmental and physiological host traits that favour their spread within aphid populations. we experimentally investigated the idea that symbionts may also modify aphid behavioural traits to enhance their transmission. aphids exhibit many behavioural defences against enemies. despite their benefits, these behaviours have some associated ... | 2011 | 21490007 |
| reca proteins from deinococcus geothermalis and deinococcus murrayi - cloning, purification and biochemical characterisation. | abstract: | 2011 | 21513512 |
| identification of prokaryotic small proteins using a comparative genomic approach. | motivation: accurate prediction of genes encoding small proteins (on the order of 50 amino acids or less) remains an elusive open problem in bioinformatics. some of the best methods for gene prediction use either sequence composition analysis or sequence similarity to a known protein coding sequence. these methods often fail for small proteins, however, either due to a lack of experimentally verified small protein coding genes or due to the limited statistical significance of statistics on small ... | 2011 | 21551138 |
| the genome of buchnera aphidicola from the aphid cinara tujafilina provides new clues about the evolutionary history of metabolic losses in bacterial endosymbionts. | the symbiotic association between aphids (homoptera) and buchnera aphidicola (γ-proteobacteria) started about 100-200 million years ago. as a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. the downsize genome process starts when the bacterium enters the host, and will probably end with its extinction and replacement by another healthier bacterium, or with the establishment of metabolic complementation between two or more bacteria. nowadays, sever ... | 2011 | 21571878 |
| non-adaptive origins of interactome complexity. | the boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation. the resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner. a key remaining question concerns the extent to which variation in the power of rando ... | 2011 | 21593762 |
| genome expansion and differential expression of amino acid transporters at the aphid/buchnera symbiotic interface. | in insects some of the most ecologically important symbioses are nutritional symbioses that provide hosts with novel traits and thereby facilitate exploitation of otherwise inaccessible niches. one such symbiosis is the ancient obligate intracellular symbiosis of aphids with the γ-proteobacteria, buchnera aphidicola. while the nutritional basis of the aphid/buchnera symbiosis is well understood, the processes and structures that mediate the intimate interactions of symbiotic partners remain unch ... | 2011 | 21613235 |
| an alternative approach to multiple genome comparison. | genome comparison is now a crucial step for genome annotation and identification of regulatory motifs. genome comparison aims for instance at finding genomic regions either specific to or in one-to-one correspondance between individuals/strains/species. it serves e.g. to pre-annotate a new genome by automatically transfering annotations from a known one. however, efficiency, flexibility and objectives of current methods do not suit the whole spectrum of applications, genome sizes and organizatio ... | 2011 | 21646341 |
| chromosomal rearrangements in salmonella enterica serovar typhi strains isolated from asymptomatic human carriers. | host-specific serovars of salmonella enterica often have large-scale chromosomal rearrangements that occur by recombination between rrn operons. two hypotheses have been proposed to explain these rearrangements: (i) replichore imbalance from horizontal gene transfer drives the rearrangements to restore balance, or (ii) the rearrangements are a consequence of the host-specific lifestyle. although recent evidence has refuted the replichore balance hypothesis, there has been no direct evidence for ... | 2011 | 21652779 |
| multimodal dynamic response of the buchnera aphidicola pleu plasmid to variations in leucine demand of its host, the pea aphid acyrthosiphon pisum. | aphids, important agricultural pests, can grow and reproduce thanks to their intimate symbiosis with the ?-proteobacterium buchnera aphidicola that furnishes them with essential amino acids lacking in their phloem sap diet. to study how b. aphidicola, with its reduced genome containing very few transcriptional regulators, responds to variations in the metabolic requirements of its host, we concentrated on the leucine metabolic pathway. we show that leucine is a limiting factor for aphid growth a ... | 2011 | 21797941 |
| cellular tropism, population dynamics, host range and taxonomic status of an aphid secondary symbiont, smls (sitobion miscanthi l type symbiont). | smls (sitobion miscanthi l type symbiont) is a newly reported aphid secondary symbiont. phylogenetic evidence from molecular markers indicates that smls belongs to the rickettsiaceae and has a sibling relationship with orientia tsutsugamushi. a comparative analysis of coxa nucleotide sequences further supports recognition of smls as a new genus in the rickettsiaceae. in situ hybridization reveals that smls is housed in both sheath cells and secondary bacteriocytes and it is also detected in aphi ... | 2011 | 21789197 |
| the legionella pneumophila chaperonin - an unusual multifunctional protein in unusual locations. | the legionella pneumophila chaperonin, high temperature protein b (htpb), was discovered as a highly immunogenic antigen, only a few years after the identification of l. pneumophila as the causative agent of legionnaires' disease. as its counterparts in other bacterial pathogens, htpb did not initially receive further attention, particularly because research was focused on a few model chaperonins that were used to demonstrate that chaperonins are essential stress proteins, present in all cellula ... | 2011 | 21713066 |
| the power of paired genomes. | species interactions are fundamental to ecology. classic studies of competition, predation, parasitism and mutualism between macroscopic organisms have provided a foundation for the discipline, but many of the most important and intimate ecological interactions are microscopic in scale. these microscopic interactions include those occurring between eukaryotic hosts and their microbial symbionts. such symbioses, ubiquitous in nature, provide experimental challenges because the partners often cann ... | 2011 | 21692233 |
| reductive evolution of bacterial genome in insect gut environment. | obligate endocellular symbiotic bacteria of insects and other organisms generally exhibit drastic genome reduction. recently, it was shown that symbiotic gut bacteria of some stinkbugs also have remarkably reduced genomes. here, we report the complete genome sequence of such a gut bacterium ishikawaella capsulata of the plataspid stinkbug megacopta punctatissima. gene repertoire and evolutionary patterns, including at richness and elevated evolutionary rate, of the 745,590 bp genome were strikin ... | 2011 | 21737395 |
| facultative symbiont infections affect aphid reproduction. | some bacterial symbionts alter their hosts reproduction through various mechanisms that enhance their transmission in the host population. in addition to its obligatory symbiont buchnera aphidicola, the pea aphid acyrthosiphon pisum harbors several facultative symbionts influencing several aspects of host ecology. aphids reproduce by cyclical parthenogenesis whereby clonal and sexual reproduction alternate within the annual life cycle. many species, including the pea aphid, also show variation i ... | 2011 | 21818272 |
| rickettsia 'in' and 'out': two different localization patterns of a bacterial symbiont in the same insect species. | intracellular symbionts of arthropods have diverse influences on their hosts, and their functions generally appear to be associated with their localization within the host. the effect of localization pattern on the role of a particular symbiont cannot normally be tested since the localization pattern within hosts is generally invariant. however, in israel, the secondary symbiont rickettsia is unusual in that it presents two distinct localization patterns throughout development and adulthood in i ... | 2011 | 21712994 |
| an at mutational bias in the tiny gc-rich endosymbiont genome of hodgkinia. | the fractional guanine + cytosine (gc) contents of sequenced bacterial genomes range from 13% to 75%. despite several decades of research aimed at understanding this wide variation, the forces controlling gc content are not well understood. recent work has suggested a universal adenine + thymine (at) mutational bias exists in all bacteria, and that the elevated gc contents found in some bacterial genomes is due to genome-wide selection for increased gc content. these results are generally consis ... | 2011 | 22113795 |
| an at mutational bias in the tiny gc-rich endosymbiont genome of hodgkinia. | the fractional guanine + cytosine (gc) contents of sequenced bacterial genomes range from 13% to 75%. despite several decades of research aimed at understanding this wide variation, the forces controlling gc content are not well understood. recent work has suggested a universal adenine + thymine (at) mutational bias exists in all bacteria, and that the elevated gc contents found in some bacterial genomes is due to genome-wide selection for increased gc content. these results are generally consis ... | 2011 | 22113795 |
| improvement of the redox balance increases l-valine production by corynebacterium glutamicum under oxygen deprivation conditions. | production of l-valine under oxygen deprivation conditions by corynebacterium glutamicum lacking the lactate dehydrogenase gene ldha and overexpressing the l-valine biosynthesis genes ilvbncde was repressed. this was attributed to imbalanced cofactor production and consumption in the overall l-valine synthesis pathway: two moles of nadh was generated and two moles of nadph was consumed per mole of l-valine produced from one mole of glucose. in order to solve this cofactor imbalance, the coenzyme ... | 2011 | 22138982 |
| detection and characterization of wolbachia infections in natural populations of aphids: is the hidden diversity fully unraveled? | aphids are a serious threat to agriculture, despite being a rather small group of insects. the about 4,000 species worldwide engage in highly interesting and complex relationships with their microbial fauna. one of the key symbionts in arthropods is wolbachia, an α-proteobacterium implicated in many important biological processes and believed to be a potential tool for biological control. aphids were thought not to harbour wolbachia; however, current data suggest that its presence in aphids has ... | 2011 | 22174869 |
| Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera. | Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein-coding regions, which are subject to ongoing inactivation and deletion. However, these same forces operate on intergenic spacers (IGSs) and affect their contents, maintenance, and rates of evolution. IGSs comprise both non-coding, non-functional regions, including decaying pseudogenes at varying stages of recognizability, as well as functional elements, such as genes for sRNAs and ... | 2011 | 21912528 |
| Influence of host phylogeographic patterns and incomplete lineage sorting on within-species genetic variability in Wigglesworthia species, obligate symbionts of tsetse flies. | Vertical transmission of obligate symbionts generates a predictable evolutionary history of symbionts that reflects that of their hosts. In insects, evolutionary associations between symbionts and their hosts have been investigated primarily among species, leaving population-level processes largely unknown. In this study, we investigated the tsetse (Diptera: Glossinidae) bacterial symbiont, Wigglesworthia glossinidia, to determine whether observed codiversification of symbiont and tsetse host sp ... | 2011 | 21948847 |
| Molecular and histological characterisation of primary (ß-proteobacteria) and secondary (?-proteobacteria) endosymbionts of three species of mealybugs (Pseudococcus longispinus, Pseudococcus calceolariae, Pseudococcus viburni) (Pseudococcidae, Hemiptera) and prediction of interactions of their GroEL homologs with Grape Leaf Roll-associated Virus-3. | Microscopic localization of endosymbiotic bacteria in three species of mealybug (Pseudococcus longispinus, long-tailed mealybug; Pseudococcus calceolariae, citrophilus mealybug; and Pseudococcus. viburni, obscure mealybug) showed these organisms were confined to bacteriocyte cells within a bacteriome centrally located within the haemocoel. Two species of bacteria were present, with the secondary endosymbiont, in all cases, living within the primary endosymbiont. DNA from the dissected bacteriome ... | 2011 | 22156418 |
| five proteins of laodelphax striatellus are potentially involved in the interactions between rice stripe virus and vector. | rice stripe virus (rsv) is the type member of the genus tenuivirus, which relies on the small brown planthopper (laodelphax striatellus fallén) for its transmission in a persistent, circulative-propagative manner. to be transmitted, virus must cross the midgut and salivary glands epithelial barriers in a transcytosis mechanism where vector receptors interact with virions, and as propagative virus, rsv need utilize host components to complete viral propagation in vector cells. at present, these m ... | 2011 | 22028913 |
| reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. | as predicted by the nearly neutral model of evolution, numerous studies have shown that reduced n(e) accelerates the accumulation of slightly deleterious changes under genetic drift. while such studies have mostly focused on eukaryotes, bacteria also offer excellent models to explore the effects of n(e). most notably, the genomes of host-dependent bacteria with small n(e) show signatures of genetic drift, including elevated k(a)/k(s). here, i explore the utility of an alternative measure of sele ... | 2011 | 22194947 |
| heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. | network analysis became a powerful tool giving new insights to the understanding of cellular behavior. heat shock, the archetype of stress responses, is a well-characterized and simple model of cellular dynamics. s. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and stress response at the gene expression level have been well characterized. however, the analysis of the reorganization of the yeast interactome during stress has not been ... | 2011 | 22022244 |
| reductive genome evolution, host-symbiont co-speciation and uterine transmission of endosymbiotic bacteria in bat flies. | bat flies of the family nycteribiidae are known for their extreme morphological and physiological traits specialized for ectoparasitic blood-feeding lifestyle on bats, including lack of wings, reduced head and eyes, adenotrophic viviparity with a highly developed uterus and milk glands, as well as association with endosymbiotic bacteria. we investigated japanese nycteribiid bat flies representing 4 genera, 8 species and 27 populations for their bacterial endosymbionts. from all the nycteribiid s ... | 2011 | 21938025 |
| reductive genome evolution, host-symbiont co-speciation and uterine transmission of endosymbiotic bacteria in bat flies. | bat flies of the family nycteribiidae are known for their extreme morphological and physiological traits specialized for ectoparasitic blood-feeding lifestyle on bats, including lack of wings, reduced head and eyes, adenotrophic viviparity with a highly developed uterus and milk glands, as well as association with endosymbiotic bacteria. we investigated japanese nycteribiid bat flies representing 4 genera, 8 species and 27 populations for their bacterial endosymbionts. from all the nycteribiid s ... | 2011 | 21938025 |
| pathogen-origin horizontally transferred genes contribute to the evolution of lepidopteran insects. | abstract: | 2011 | 22151541 |
| host preference between symbiotic and aposymbiotic aphis fabae, by the aphid parasitoid, lysiphlebus ambiguus. | few empirical studies have directly explored the association between buchnera aphidicola (enterobacteriales: enterobacteriaceae), the primary endosymbiont of aphids, and the life history strategies of aphid parasitoids. a series of paired-choice experiments were conducted to explore the preference of the parasitoid lysiphlebus ambiguus halliday (hymenoptera: aphididae) for symbiotic and aposymbiotic aphis fabae scopoli (hemiptera: aphididae) and the suitability of these hosts for parasitoid deve ... | 2011 | 21870967 |
| the metj regulon in gammaproteobacteria determined by comparative genomics methods. | whole-genome sequencing of bacteria has proceeded at an exponential pace but annotation validation has lagged behind. for instance, the metj regulon, which controls methionine biosynthesis and transport, has been studied almost exclusively in e. coli and salmonella, but homologs of metj exist in a variety of other species. these include some that are pathogenic (e.g. yersinia) and some that are important for environmental remediation (e.g. shewanella) but many of which have not been extensively ... | 2011 | 22082356 |
| dynamics of genome evolution in facultative symbionts of aphids. | aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist buchnera plus several bacteria that are not required for host survival. among the latter, 'candidatus regiella insecticola' and 'candidatus hamiltonella defensa' are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. we have sequenced almost the entire genome of r. insecticola (2.07 mbp) and compared it with the recently published ... | 2010 | 21966902 |
| Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. | The genome sequencing of Buchnera aphidicola BCc from the aphid Cinara cedri, which is the smallest known Buchnera genome, revealed that this bacterium had lost its symbiotic role, as it was not able to synthesize tryptophan and riboflavin. Moreover, the biosynthesis of tryptophan is shared with the endosymbiont Serratia symbiotica SCc, which coexists with B. aphidicola in this aphid. The whole-genome sequencing of S. symbiotica SCc reveals an endosymbiont in a stage of genome reduction that is ... | 2011 | 22102823 |
| purifying selection, sequence composition and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. | comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. here, we explored genomic variation within blochmannia vafer, an obligate mutualist of the ant camponotus vafer. polymorphism analysis of the illumina dataset used previously ... | 2011 | 22117087 |
| purifying selection, sequence composition and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. | comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. here, we explored genomic variation within blochmannia vafer, an obligate mutualist of the ant camponotus vafer. polymorphism analysis of the illumina dataset used previously ... | 2011 | 22117087 |
| Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities. | Cockroaches (Blattaria: Dictyoptera) harbor the endosymbiont Blattabacterium sp. in their abdominal fat body. This endosymbiont is involved in nitrogen recycling and amino acid provision to its host. In this study, the genome of Blattabacterium sp. of Cryptocercus punctulatus (BCpu) was sequenced and compared with those of the symbionts of Blattella germanica and Periplaneta americana, BBge and BPam, respectively. The BCpu genome consists of a chromosome of 605.7 kb and a plasmid of 3.8 kb and i ... | 2011 | 22094859 |
| decoding in candidatus riesia pediculicola, close to a minimal trna modification set? | a comparative genomic analysis of the recently sequenced human body louse unicellular endosymbiont candidatus riesia pediculicola with a reduced genome (582 kb), revealed that it is the only known organism that might have lost all post-transcriptional base and ribose modifications of the trna body, retaining only modifications of the anticodon-stem-loop essential for mrna decoding. such a minimal trna modification set was not observed in other insect symbionts or in parasitic unicellular bacteri ... | 2012 | 23308034 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| dcia is an ancestral replicative helicase operator essential for bacterial replication initiation. | delivery of the replicative helicase onto dna is an essential step in the initiation of replication. in bacteria, dnac (in escherichia coli) and dnai (in bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnac and dnai (dna[ci]) are present in only a few bacterial phyla. we show that dna[ci] was domesticated at least seve ... | 2016 | 27830752 |
| preferential interaction of the his pause rna hairpin with rna polymerase beta subunit residues 904-950 correlates with strong transcriptional pausing. | rna secondary structures (hairpins) that form as the nascent rna emerges from rna polymerase are important components of many signals that regulate transcription, including some pause sites, all rho-independent terminators, and some antiterminators. at the his leader pause site, a 5-bp-stem, 8-nt-loop pause rna hairpin forms 11 nt from the rna 3' end and stabilizes a transcription complex conformation slow to react with ntp substrate. this stabilization appears to depend at least in part on an i ... | 1997 | 9237994 |
| calibrating bacterial evolution. | attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal applica ... | 1999 | 10535975 |
| optimality of the genetic code with respect to protein stability and amino-acid frequencies. | the genetic code is known to be efficient in limiting the effect of mistranslation errors. a misread codon often codes for the same amino acid or one with similar biochemical properties, so the structure and function of the coded protein remain relatively unaltered. previous studies have attempted to address this question quantitatively, by estimating the fraction of randomly generated codes that do better than the genetic code in respect of overall robustness. we extended these results by inves ... | 2001 | 11737948 |
| comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. | a comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. thirty-four r-protein families are represented in all domains but 33 families are specific to archaea and eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to archaea and eukaryotes. with only one specific r-protein, the arch ... | 2002 | 12490706 |
| abstracts of the fourth international symposium on molecular insect science. may 28-june 2, 2002. tucson, arizona, usa. | | 2002 | 15455051 |
| evolution of gene fusions: horizontal transfer versus independent events. | gene fusions can be used as tools for functional prediction and also as evolutionary markers. fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution. | 2002 | 12049665 |
| alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network. | alpha-crystallins were originally recognized as proteins contributing to the transparency of the mammalian eye lens. subsequently, they have been found in many, but not all, members of the archaea, bacteria, and eucarya. most members of the diverse alpha-crystallin family have four common structural and functional features: (i) a small monomeric molecular mass between 12 and 43 kda; (ii) the formation of large oligomeric complexes; (iii) the presence of a moderately conserved central region, the ... | 2002 | 11875128 |
| ccpa-dependent carbon catabolite repression in bacteria. | carbon catabolite repression (ccr) by transcriptional regulators follows different mechanisms in gram-positive and gram-negative bacteria. in gram-positive bacteria, ccpa-dependent ccr is mediated by phosphorylation of the phosphoenolpyruvate:sugar phosphotransferase system intermediate hpr at a serine residue at the expense of atp. the reaction is catalyzed by hpr kinase, which is activated by glycolytic intermediates. in this review, the distribution of ccpa-dependent ccr among bacteria is inv ... | 2003 | 14665673 |
| functionality of system components: conservation of protein function in protein feature space. | many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties. we show here that such protein features are more conserved among orthologs than paralogs, indicating they are crucial for protein function and thus subject to selective pressure. this means that a function prediction method based on sequence-derived features may be able to discriminate between protei ... | 2003 | 14559779 |
| ancient origin of the tryptophan operon and the dynamics of evolutionary change. | the seven conserved enzymatic domains required for tryptophan (trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. a comparative bioinformatics evaluation of the conservation and organization of the genes of trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and oper ... | 2003 | 12966138 |
| hgt-db: a database of putative horizontally transferred genes in prokaryotic complete genomes. | the horizontal gene transfer database (hgt-db) is a genomic database that includes statistical parameters such as g+c content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. the current version of the database contains 88 bacterial and arch ... | 2003 | 12519978 |
| inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy. | the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ... | 2004 | 15214963 |
| sequence motifs that distinguish atp(ctp):trna nucleotidyl transferases from eubacterial poly(a) polymerases. | atp(ctp):trna nucleotidyl transferases, trna maturing enzymes found in all organisms, and eubacterial poly(a) polymerases, enzymes involved in mrna degradation, are so similar that until now their biochemical functions could not be distinguished by their amino acid sequence. blast searches and analysis with the program "sequence space" for the prediction of functional residues revealed sequence motifs which define these two protein families. one of the poly(a) polymerase defining motifs specifie ... | 2004 | 15146073 |
| prediction of rna-binding proteins from primary sequence by a support vector machine approach. | elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. computational methods have been developed for the prediction of protein-protein interactions. but insufficient attention has been paid to the prediction of protein-rna interactions, which play central roles in regulating gene expression and certain rna-mediated enzymatic processes. this work explored the use of a machine learning method, support vector machines (svm) ... | 2004 | 14970381 |
| comparative genomic analyses of the bacterial phosphotransferase system. | we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ... | 2005 | 16339738 |
| protein length in eukaryotic and prokaryotic proteomes. | we analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. comparing eukaryotes and prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. the magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended m ... | 2005 | 15951512 |
| identification of genomic features using microsyntenies of domains: domain teams. | the detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). our approach adopts the technique of temporarily forgetting genes and working directly with p ... | 2005 | 15899966 |
| systematic association of genes to phenotypes by genome and literature mining. | one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ... | 2005 | 15799710 |
| coverage of whole proteome by structural genomics observed through protein homology modeling database. | we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ... | 2006 | 17146617 |
| comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms. | hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ... | 2006 | 16780600 |
| phylogenomic analysis of the giy-yig nuclease superfamily. | the giy-yig domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-ltr retrotransposons) and in enzymes involved in dna repair and recombination. however, to date no systematic search for novel members of the giy-yig superfamily or comparative analysis of these enzymes has been reported. | 2006 | 16646971 |
| a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins. | lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ... | 2006 | 16585737 |
| paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms. | while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ... | 2006 | 16529662 |
| algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. | comparison of metabolic networks is typically performed based on the organisms' enzyme contents. this approach disregards functional replacements as well as orthologies that are misannotated. direct comparison of the structure of metabolic networks can circumvent these problems. | 2006 | 16478540 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| transcriptional regulatory network discovery via multiple method integration: application to e. coli k12. | transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ... | 2007 | 17397539 |
| 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 |
| rnrdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to genbank. | ribonucleotide reductases (rnrs) catalyse the only known de novo pathway for deoxyribonucleotide synthesis, and are therefore essential to dna-based life. while ribonucleotide reduction has a single evolutionary origin, significant differences between rnrs nevertheless exist, notably in cofactor requirements, subunit composition and allosteric regulation. these differences result in distinct operational constraints (anaerobicity, iron/oxygen dependence and cobalamin dependence), and form the bas ... | 2009 | 19995434 |
| meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. | in the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the tree of life (tol). underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity ... | 2012 | 22915837 |
| composition and seasonal variation of rhipicephalus turanicus and rhipicephalus sanguineus bacterial communities. | a 16s rrna gene approach, including 454 pyrosequencing and quantitative pcr (qpcr), was used to describe the bacterial community in rhipicephalus turanicus and to evaluate the dynamics of key bacterial tenants of adult ticks during the active questing season. the bacterial community structure of rh. turanicus was characterized by high dominance of coxiella and rickettsia and extremely low taxonomic diversity. parallel diagnostic pcr further revealed a novel coxiella species which was present and ... | 2012 | 22467507 |
| comparing the similarity of different groups of bacteria to the human proteome. | numerous aspects of the relationship between bacteria and human have been investigated. one aspect that has recently received attention is sequence overlap at the proteomic level. however, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, g-c content, and proteome size. in this study, we began by performing a general characterization of the range of ... | 2012 | 22558081 |
| microbial lifestyle and genome signatures. | microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. the genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. the present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. niche-specific signatures identified at different leve ... | 2012 | 23024607 |
| statistics for approximate gene clusters. | genes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. the computational detection of these patterns, which are usually referred to as gene clusters, has become increasingly sensitive over the past decade. the most powerful approaches allow for various types of imperfect cluster conservation: cluster locations may be internally rearranged. the individual cluster locations may contain ... | 2013 | 24564620 |
| the embedding problem for markov models of nucleotide substitution. | continuous-time markov processes are often used to model the complex natural phenomenon of sequence evolution. to make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. the validity of one such assumption, time-homogeneity, has never been explored. violations of this assumption can be found by identifying non-embeddability. a process is non-embeddable if it can not be embedded in a continuous time-homogen ... | 2013 | 23935949 |
| identification of novel adhesins of m. tuberculosis h37rv using integrated approach of multiple computational algorithms and experimental analysis. | pathogenic bacteria interacting with eukaryotic host express adhesins on their surface. these adhesins aid in bacterial attachment to the host cell receptors during colonization. a few adhesins such as heparin binding hemagglutinin adhesin (hbha), apa, malate synthase of m. tuberculosis have been identified using specific experimental interaction models based on the biological knowledge of the pathogen. in the present work, we carried out computational screening for adhesins of m. tuberculosis. ... | 2013 | 23922800 |
| circular helix-like curve: an effective tool of biological sequence analysis and comparison. | this paper constructed a novel injection from a dna sequence to a 3d graph, named circular helix-like curve (chc). the presented graphical representation is available for visualizing characterizations of a single dna sequence and identifying similarities and differences among several dnas. a 12-dimensional vector extracted from chc, as a numerical characterization of chc, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal rnas, 48 hepatitis e viruses, and 18 eutherian ... | 2016 | 27403205 |
| challenges with using names to link digital biodiversity information. | | 2016 | 27346955 |
| origin and evolution of rickettsial plasmids. | rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. despite their allopatric lifestyle, almost half of the 26 currently validated rickettsia species have plasmids. in order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and no ... | 2016 | 26866478 |
| the effect of sequencing errors on metagenomic gene prediction. | gene prediction is an essential step in the annotation of metagenomic sequencing reads. since most metagenomic reads cannot be assembled into long contigs, specialized statistical gene prediction tools have been developed for short and anonymous dna fragments, e.g. metageneannotator and orphelia. while conventional gene prediction methods have been subject to a benchmark study on real sequencing reads with typical errors, such a comparison has not been conducted for specialized tools, yet. their ... | 2009 | 19909532 |
| distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. | it is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. recent sequence assignment techniques have achieved high levels of ... | 2010 | 20333228 |
| the accelerating convergence of genomics and microbiology. | | 2001 | 11305936 |
| intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host. | we investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four microcerotermes species (termitidae) and four reticulitermes species (rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16s rrna. the obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. both analyses revealed that the bacterial community structure was remarka ... | 2005 | 16269686 |
| the subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. | the release of the 1000th complete microbial genome will occur in the next two to three years. in anticipation of this milestone, the fellowship for interpretation of genomes (fig) launched the project to annotate 1000 genomes. the project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of t ... | 2005 | 16214803 |
| gismo--gene identification using a support vector machine for orf classification. | we present the novel prokaryotic gene finder gismo, which combines searches for protein family domains with composition-based classification based on a support vector machine. gismo is highly accurate; exhibiting high sensitivity and specificity in gene identification. we found that it performs well for complete prokaryotic chromosomes, irrespective of their gc content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. using gismo, we found se ... | 2006 | 17175534 |
| gismo--gene identification using a support vector machine for orf classification. | we present the novel prokaryotic gene finder gismo, which combines searches for protein family domains with composition-based classification based on a support vector machine. gismo is highly accurate; exhibiting high sensitivity and specificity in gene identification. we found that it performs well for complete prokaryotic chromosomes, irrespective of their gc content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. using gismo, we found se ... | 2006 | 17175534 |
| 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 |
| massive comparative genomic analysis reveals convergent evolution of specialized bacteria. | genome size and gene content in bacteria are associated with their lifestyles. obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. the growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacte ... | 2009 | 19361336 |
| 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 |