| extensive repetitive dna facilitates prokaryotic genome plasticity. | prokaryotic genomes are substantially diverse, even when from closely related species, with the resulting phenotypic diversity representing a repertoire of adaptations to specific constraints. within the microbial population, genome content may not be fixed, as changing selective forces favor particular phenotypes; however, organisms well adapted to particular niches may have evolved mechanisms to facilitate such plasticity. the highly diverse helicobacter pylori is a model for studying genome p ... | 2003 | 14593200 |
| enzyme-specific profiles for genome annotation: priam. | the advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. here we describe priam, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the enzyme database. priam relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each enzyme entry. automatically generated logical rules define which of these profile ... | 2003 | 14602924 |
| a key role for the mrna leader structure in translational control of ribosomal protein s1 synthesis in gamma-proteobacteria. | the translation initiation region (tir) of the escherichia coli rpsa mrna coding for ribosomal protein s1 is characterized by a remarkable efficiency in driving protein synthesis despite the absence of the canonical shine-dalgarno element, and by a strong and specific autogenous repression in the presence of free s1 in trans. the efficient and autoregulated e.coli rpsa tir comprises not less than 90 nt upstream of the translation start and can be unambiguously folded into three irregular hairpin ... | 2003 | 14627832 |
| growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis p) in escherichia coli. | the intracellular concentration of the escherichia coli factor for inversion stimulation (fis), a global regulator of transcription and a facilitator of certain site-specific dna recombination events, varies substantially in response to changes in the nutritional environment and growth phase. under conditions of nutritional upshift, fis is transiently expressed at very high levels, whereas under induced starvation conditions, fis is repressed by stringent control. we show that both of these regu ... | 2004 | 14679232 |
| a conservative test of genetic drift in the endosymbiotic bacterium buchnera: slightly deleterious mutations in the chaperonin groel. | the obligate endosymbiotic bacterium buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. because buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. recent studies of intraspecific variation in buchnera reveal patterns consistent with this hypo ... | 2003 | 14704156 |
| changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont buchnera in an aphid. | almost all aphids harbour an endosymbiotic bacterium, buchnera aphidicola, in bacteriocytes. buchnera synthesizes essential nutrients and supports growth and reproduction of the host. over the long history of endosymbiosis, many essential genes have been lost from the buchnera genome, resulting in drastic genome reduction and the inability to live outside the host cells. in turn, when deprived of buchnera, the host aphid suffers retarded growth and sterility. buchnera and the host aphid are ofte ... | 2003 | 14728775 |
| cassette-like variation of restriction enzyme genes in escherichia coli c and relatives. | a surprising result of comparative bacterial genomics has been the large amount of dna found to be present in one strain but not in another of the same species. we examine in detail one location where gene content varies extensively, the restriction cluster in escherichia coli. this region is designated the immigration control region (icr) for the density and variability of restriction functions found there. to better define the boundaries of this variable locus, we determined the sequence of th ... | 2004 | 14744977 |
| host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. | bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. candidatus blochmannia gen. nov. (blochmannia) is an obligate bacterial associate of camponotus and related ant genera (hymenoptera: formicidae). the occurrence of blochmannia in all camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, sta ... | 2004 | 14965905 |
| evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of paederus fuscipes beetles. | pederin belongs to a group of antitumor compounds found in terrestrial beetles and marine sponges. it is used by apparently all members of the rove beetle genera paederus and paederidus as a chemical defense against predators. however, a recent analysis of the putative pederin biosynthesis (ped) gene cluster strongly suggests that pederin is produced by bacterial symbionts. we have sequenced an extended region of the symbiont genome to gain further insight into the biology of this as-yet-uncultu ... | 2004 | 14973122 |
| a phylogenomic study of endosymbiotic bacteria. | endosymbiotic bacteria of aphids, buchnera aphidicola, and tsetse flies, wigglesworthia glossinidia, are descendents of free-living gamma-proteobacteria. the acceleration of sequence evolution in the endosymbiont genomes is here estimated from a phylogenomic analysis of the gamma-proteobacteria. the tree topologies associated with the most highly conserved genes suggest that the endosymbionts form a sister group with escherichia coli, salmonella sp., and yersinia pestis. our results indicate tha ... | 2004 | 15014155 |
| comparative genomics of gene-family size in closely related bacteria. | the wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. | 2004 | 15059260 |
| transgenic expression of reca of the spirochetes borrelia burgdorferi and borrelia hermsii in escherichia coli revealed differences in dna repair and recombination phenotypes. | after unsuccessful attempts to recover a viable reca-deficient mutant of the lyme borreliosis agent borrelia burgdorferi, we characterized the functional activities of reca of b. burgdorferi, as well as reca of the relapsing fever spirochete borrelia hermsii and the free-living spirochete leptospira biflexa, in a reca mutant of escherichia coli. as a control, e. coli reca was expressed from the same plasmid vector. dna damage repair activity was assessed after exposure of the transgenic cells to ... | 2004 | 15060027 |
| properties of bacillus subtilis sigma a factors with region 1.1 and the conserved arg-103 at the n terminus of region 1.2 deleted. | sigma factors in the sigma(70) family can be classified into the primary and alternative sigma factors according to their physiological functions and amino acid sequence similarities. the primary sigma factors are composed of four conserved regions, with the conserved region 1 being divided into two subregions. region 1.1, which is absent from the alternative sigma factor, is poor in conservation; however, region 1.2 is well conserved. we investigated the importance of these two subregions to th ... | 2004 | 15060039 |
| analysis of an engineered salmonella flagellar fusion protein, flir-flhb. | salmonella flir and flhb are membrane proteins necessary for flagellar export. in clostridium a flir-flhb fusion gene exists. we constructed a similar salmonella fusion gene which is able to complement flir, flhb, and flir flhb null strains. western blotting revealed that the flir-flhb fusion protein retains the flhb protein's cleavage properties. we conclude that the flir and flhb proteins are physically associated in the wild-type salmonella basal body, probably in a 1:1 ratio. | 2004 | 15060055 |
| fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy. | a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ... | 2004 | 15060178 |
| assessment of 35mer amino-modified oligonucleotide based microarray with bacterial samples. | parallel quantification of a large number of messenger rna transcripts, using microarray technology, promises to provide unsuspected information about many cellular processes. although experimental protocols on microarray applications are available, only limited methodological information on glass-slide manufacturing and signal interpretation has been published. the aim of this paper is to provide new insights into the practical aspects of the construction and hybridization of oligonucleotide-ba ... | 2004 | 15063061 |
| microorganisms resistant to free-living amoebae. | free-living amoebae feed on bacteria, fungi, and algae. however, some microorganisms have evolved to become resistant to these protists. these amoeba-resistant microorganisms include established pathogens, such as cryptococcus neoformans, legionella spp., chlamydophila pneumoniae, mycobacterium avium, listeria monocytogenes, pseudomonas aeruginosa, and francisella tularensis, and emerging pathogens, such as bosea spp., simkania negevensis, parachlamydia acanthamoebae, and legionella-like amoebal ... | 2004 | 15084508 |
| evolution of the leucine gene cluster in buchnera aphidicola: insights from chromosomal versions of the cluster. | in buchnera aphidicola strains associated with the aphid subfamilies thelaxinae, lachninae, pterocommatinae, and aphidinae, the four leucine genes (leua, -b, -c, and -d) are located on a plasmid. however, these genes are located on the main chromosome in b. aphidicola strains associated with the subfamilies pemphiginae and chaitophorinae. the sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in b. aphidicola strains a ... | 2004 | 15090505 |
| prolinks: a database of protein functional linkages derived from coevolution. | the advent of whole-genome sequencing has led to methods that infer protein function and linkages. we have combined four such algorithms (phylogenetic profile, rosetta stone, gene neighbor and gene cluster) in a single database--prolinks--that spans 83 organisms and includes 10 million high-confidence links. the proteome navigator tool allows users to browse predicted linkage networks interactively, providing accompanying annotation from public databases. the prolinks database and the proteome n ... | 2004 | 15128449 |
| a novel alpha-proteobacterium resides in the mitochondria of ovarian cells of the tick ixodes ricinus. | an intracellular bacterium from ixodes ricinus ticks collected in italy was characterized by electron microscopy (em), pcr sequencing of the 16s rrna gene, molecular phylogenetic analysis, and in situ hybridization (ish). this bacterium was shown by em to be present in the cytoplasm, as well as in the mitochondria of ovarian cells. when universal 16s rrna bacterial primers were used, pcr amplification of ovarian dna followed by cloning and sequencing resulted in the same sequence being found in ... | 2004 | 15128508 |
| bacterial genomes as new gene homes: the genealogy of orfans in e. coli. | differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. however, most bacteria contain large numbers of orfans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. the uniqueness of orfans within a genome has precluded the use of a comparative approach to examine their function and evolution. however, by identifying sequences unique to monophyletic g ... | 2004 | 15173110 |
| evolutionary relationships of primary prokaryotic endosymbionts of whiteflies and their hosts. | whiteflies (hemiptera: sternorrhyncha: aleyrodidae) are plant sap-sucking insects that harbor prokaryotic primary endosymbionts (p-endosymbionts) within specialized cells located in their body cavity. four-kilobase dna fragments containing 16s-23s ribosomal dna (rdna) were amplified from the p-endosymbiont of 24 whiteflies from 22 different species of 2 whitefly subfamilies. in addition, 3-kb dna fragments containing mitochondrial cytb, nd1, and large-subunit rdna (lrdna) were amplified from 17 ... | 2004 | 15184137 |
| replication of the endosymbiotic bacterium blochmannia floridanus is correlated with the developmental and reproductive stages of its ant host. | the dynamics of replication of the intracellular endosymbiotic bacterium blochmannia floridanus was determined during the larval development of its host ant camponotus floridanus by real-time quantitative pcr. the bacteria were found to proliferate during pupation and immediately after the eclosion of the imagines (adult ants). in older workers the number of bacteria present in the midgut bacteriocytes decreased significantly. in contrast, the bacterial population in the ovaries was dependent on ... | 2004 | 15240288 |
| the evolutionary fate of nonfunctional dna in the bacterial endosymbiont buchnera aphidicola. | reduction of the genome size in endosymbiotic bacteria is the main feature linked to the adaptation to a host-associated lifestyle. we have analyzed the fate of the nonfunctional dna in buchnera aphidicola, the primary endosymbiont of aphids. at least 164 gene losses took place during the recent evolution of three b. aphidicola strains, symbionts of the aphids acyrthosiphon pisum (bap), schizaphis graminum (bsg), and baizongia pistacia (bbp). a typical pattern starts with the inactivation of a g ... | 2004 | 15317875 |
| coexistence of wolbachia with buchnera aphidicola and a secondary symbiont in the aphid cinara cedri. | intracellular symbiosis is very common in the insect world. for the aphid cinara cedri, we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. pcr amplification and sequencing of the 16s ribosomal dna (rdna) genes showed that, in addition to harboring buchnera aphidicola, the primary endosymbiont of aphids, c. cedri harbors a secondary symbiont (s symbiont) that was previously found to be associat ... | 2004 | 15375144 |
| crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis. | gamma-glutamylcysteine synthetase (gammagcs), a rate-limiting enzyme in glutathione biosynthesis, plays a central role in glutathione homeostasis and is a target for development of potential therapeutic agents against parasites and cancer. we have determined the crystal structures of escherichia coli gammagcs unliganded and complexed with a sulfoximine-based transition-state analog inhibitor at resolutions of 2.5 and 2.1 a, respectively. in the crystal structure of the complex, the bound inhibit ... | 2004 | 15477603 |
| analysis of the cytoplasmic domains of salmonella flha and interactions with components of the flagellar export machinery. | most flagellar proteins are exported via a type iii export apparatus which, in part, consists of the membrane proteins flha, flhb, flio, flip, fliq, and flir and is housed within the membrane-supramembrane ring formed by flif subunits. salmonella flha is a 692-residue integral membrane protein with eight predicted transmembrane spans. its function is not understood, but it is necessary for flagellar export. we have created mutants in which potentially important sequences were deleted. flha lacki ... | 2004 | 15516571 |
| a genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. | the timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. however, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. we assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species ... | 2004 | 15535883 |
| structural similarity of ybed protein from escherichia coli to allosteric regulatory domains. | lipoic acid is an essential prosthetic group in several metabolic pathways. the biosynthetic pathway of protein lipoylation in escherichia coli involves gene products of the lip operon. ybed is a conserved bacterial protein located in the daca-lipb intergenic region. here, we report the nuclear magnetic resonance structure of ybed from e. coli. the structure includes a beta alpha beta beta alpha beta fold with two alpha-helices on one side of a four-strand antiparallel beta-sheet. the beta 2-bet ... | 2004 | 15547281 |
| evolutionary relationships of fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. | the phylogenetic position and evolutionary relationships of fusobacteria remain uncertain. especially intriguing is their relatedness to low g+c gram positive bacteria (firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. taking advantage of the recent completion of the fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of fusobacterium genes by phylogenetic analysis and comparative genomics tools. | 2004 | 15566569 |
| the rpoh-mediated stress response in neisseria gonorrhoeae is regulated at the level of activity. | the general stress response in neisseria gonorrhoeae was investigated. transcriptional analyses of the genes encoding the molecular chaperones dnak, dnaj, and grpe suggested that they are transcribed from sigma32 (rpoh)-dependent promoters upon exposure to stress. this was confirmed by mutational analysis of the sigma32 promoter of dnak. the gene encoding the gonococcal rpoh sigma factor appears to be essential, as we could not isolate viable mutants. deletion of an unusually long rpoh leader se ... | 2004 | 15576794 |
| new insights into type ii nad(p)h:quinone oxidoreductases. | type ii nad(p)h:quinone oxidoreductases (ndh-2) catalyze the two-electron transfer from nad(p)h to quinones, without any energy-transducing site. ndh-2 accomplish the turnover of nad(p)h, regenerating the nad(p)(+) pool, and may contribute to the generation of a membrane potential through complexes iii and iv. these enzymes are usually constituted by a nontransmembrane polypeptide chain of approximately 50 kda, containing a flavin moiety. there are a few compounds that can prevent their activity ... | 2004 | 15590775 |
| metabolic interdependence of obligate intracellular bacteria and their insect hosts. | mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. however, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell. this review attempts to provide insights into the complex physiological interactions and the evolution of m ... | 2004 | 15590782 |
| mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome. | the influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. here, we explore the impact of mutation and selection on the dynamics of synonymous changes in buchnera aphidicola, the at-rich bacterial endosymbiont of aphids. specifically, we evaluated three ... | 2004 | 15599516 |
| tractor_db: a database of regulatory networks in gamma-proteobacterial genomes. | experimental data on the escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (tfs), tfs' binding sites and operons) within its genome. as more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcrip ... | 2005 | 15608293 |
| tractor_db: a database of regulatory networks in gamma-proteobacterial genomes. | experimental data on the escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (tfs), tfs' binding sites and operons) within its genome. as more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcrip ... | 2005 | 15608293 |
| differences in codon bias cannot explain differences in translational power among microbes. | translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. one factor known to affect translational power is biased use of synonymous codons. the correlation within an organism between expression level and degree of codon bias among genes of escherichia coli and other bact ... | 2005 | 15636642 |
| accelerated evolution associated with genome reduction in a free-living prokaryote. | three complete genomes of prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in g+c content. as all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in prochlorococcus is the first documen ... | 2005 | 15693943 |
| pseudomonas aeruginosa mutl protein functions in escherichia coli. | escherichia coli muts, mutl and muth proteins act sequentially in the mmrs (mismatch repair system). muth directs the repair system to the newly synthesized strand due to its transient lack of dam (dna-adenine methylase) methylation. although pseudomonas aeruginosa does not have the corresponding e. coli muth and dam homologues, and consequently the mmrs seems to work differently, we show that the mutl gene from p. aeruginosa is capable of complementing a mutl-deficient strain of e. coli. mutl f ... | 2005 | 15709980 |
| comparative analysis of two genomic regions among four strains of buchnera aphidicola, primary endosymbiont of aphids. | preliminary analysis of two selected genomic regions of buchnera aphidicola bcc, the primary endosymbiont of the cedar aphid cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three b. aphidicola genomes previously sequenced, that are associated with different aphid species. both regions exhibit a significant reduction in length and gene number in b. aphidicola bcc, as it could be expected since it possess the smallest bacte ... | 2004 | 15716086 |
| variation in the strength of selected codon usage bias among bacteria. | among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. however, in other species selection appears to have been ineffective. here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. the approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. the ... | 2005 | 15728743 |
| bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion. | like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ... | 2005 | 15757514 |
| genome rearrangement distances and gene order phylogeny in gamma-proteobacteria. | genome rearrangements have been studied in 30 gamma-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. this set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. genome rearrangement distances were estimated based on either the number of breakpoints or the minimal number of inversions separating two genomes. ... | 2005 | 15772379 |
| the wolbachia genome of brugia malayi: endosymbiont evolution within a human pathogenic nematode. | complete genome dna sequence and analysis is presented for wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode brugia malayi. although, quantitatively, the genome is even more degraded than those of closely related rickettsia species, wolbachia has retained more intact metabolic pathways. the ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be wolbachia's principal co ... | 2005 | 15780005 |
| solution structure of the carbon storage regulator protein csra from escherichia coli. | the carbon storage regulator a (csra) is a protein responsible for the repression of a variety of stationary-phase genes in bacteria. in this work, we describe the nuclear magnetic resonance (nmr)-based structure of the csra dimer and its rna-binding properties. csra is a dimer of two identical subunits, each composed of five strands, a small alpha-helix and a flexible c terminus. nmr titration experiments suggest that the beta1-beta2 and beta3-beta4 loops and the c-terminal helix are important ... | 2005 | 15866937 |
| global divergence of microbial genome sequences mediated by propagating fronts. | we model the competition between homologous recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. depending on the specifics of homologous recombination, we find that global sequence divergence can be mediated by fronts propagating along the genome, whose characteristic signature on genome structure is elucidated, and apparently observed in closely related bacillus strains. front propagation provides an em ... | 2005 | 15878987 |
| a multidomain fusion protein in listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis. | glutathione is the predominant low-molecular-weight peptide thiol present in living organisms and plays a key role in protecting cells against oxygen toxicity. until now, glutathione synthesis was thought to occur solely through the consecutive action of two physically separate enzymes, gamma-glutamylcysteine ligase and glutathione synthetase. in this report we demonstrate that listeria monocytogenes contains a novel multidomain protein (termed gshf) that carries out complete synthesis of glutat ... | 2005 | 15901709 |
| prediction of functional modules based on comparative genome analysis and gene ontology application. | we present a computational method for the prediction of functional modules encoded in microbial genomes. in this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. we first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and gene ontology ass ... | 2005 | 15901854 |
| evolutionary relationships of three new species of enterobacteriaceae living as symbionts of aphids and other insects. | ecological studies on three bacterial lineages symbiotic in aphids have shown that they impose a variety of effects on their hosts, including resistance to parasitoids and tolerance to heat stress. phylogenetic analyses of partial sequences of gyrb and reca are consistent with previous analyses limited to 16s rrna gene sequences and yield improved confidence of the evolutionary relationships of these symbionts. all three symbionts are in the enterobacteriaceae. one of the symbionts, here given t ... | 2005 | 15933033 |
| regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont buchnera aphidicola. | buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. using full-genome microarrays for b. aphidicola of the host schizaphis graminum, we examined transcriptome respon ... | 2005 | 15937185 |
| the genome sequence of rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. | we sequenced the genome of rickettsia felis, a flea-associated obligate intracellular alpha-proteobacterium causing spotted fever in humans. besides a circular chromosome of 1,485,148 bp, r. felis exhibits the first putative conjugative plasmid identified among obligate intracellular bacteria. this plasmid is found in a short (39,263 bp) and a long (62,829 bp) form. r. felis contrasts with previously sequenced rickettsia in terms of many other features, including a number of transposases, severa ... | 2005 | 15984913 |
| extrachromosomal dna of the symbiont sodalis glossinidius. | the extrachromosomal dna of sodalis glossinidius from two tsetse fly species was sequenced and contained four circular elements: three plasmids, psg1 (82 kb), psg2 (27 kb), and psg4 (11 kb), and a bacteriophage-like psg3 (19 kb) element. the information suggests s. glossinidius is evolving towards an obligate association with tsetse flies. | 2005 | 15995217 |
| systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. | public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. the available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. | 2005 | 16011797 |
| mosaic nature of the wolbachia surface protein. | lateral gene transfer and recombination play important roles in the evolution of many parasitic bacteria. here we investigate intragenic recombination in wolbachia bacteria, considered among the most abundant intracellular bacteria on earth. we conduct a detailed analysis of the patterns of variation and recombination within the wolbachia surface protein, utilizing an extensive set of published and new sequences from five main supergroups of wolbachia. analysis of nucleotide and amino acid seque ... | 2005 | 16030235 |
| the bacteriophage p1 hot gene product can substitute for the escherichia coli dna polymerase iii {theta} subunit. | the theta subunit (hole gene product) of escherichia coli dna polymerase (pol) iii holoenzyme is a tightly bound component of the polymerase core. within the core (alpha-epsilon-theta), the alpha and epsilon subunits carry the dna polymerase and 3' proofreading functions, respectively, while the precise function of theta is unclear. hole homologs are present in genomes of other enterobacteriae, suggestive of a conserved function. putative homologs have also been found in the genomes of bacteriop ... | 2005 | 16077097 |
| phylogenetic analysis of pasteuria penetrans by use of multiple genetic loci. | pasteuria penetrans is a gram-positive, endospore-forming eubacterium that apparently is a member of the bacillus-clostridium clade. it is an obligate parasite of root knot nematodes (meloidogyne spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. consequently, p. penetrans has long been recognized as a potential biocontrol agent for root knot nematode ... | 2005 | 16077116 |
| resistance is costly: trade-offs between immunity, fecundity and survival in the pea aphid. | parasitoids are among the most important natural enemies of insects in many environments. acyrthosiphon pisum, the pea aphid, is a common pest of the leguminous crops in temperate regions. pea aphids are frequently attacked by a range of endoparasitic wasps, including the common aphidiine, aphidius ervi. immunity to parasitoid attack is thought to involve secondary symbiotic bacteria, the presence of which is associated with the death of the parasitoid egg. it has been suggested that there is a ... | 2005 | 16096092 |
| bacterial genome size reduction by experimental evolution. | bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. here we examined the rate and process of genome reduction in the bacterium salmonella enterica by a serial passage experimental evolution procedure. the initial rate of dna loss was estimated to be 0.05 bp per chromosome per generation for a wt bacterium and approximately 50-fold higher for a muts mutant defective in methyl-dire ... | 2005 | 16099836 |
| a stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization. | we have determined the effect of mutations involving isoleucine and valine (i.e., mutations i-->v and v-->i) on the stability of escherichia coli thioredoxin. despite the similarity in chemical structure (v and i differ only in a methyl group), we find that many environments are optimized to a significant extent for either v or i. we find, furthermore, that a plot of effect of hydrophobic mutations on stability versus packing density shows a strikingly simple pattern that clearly reflects evolut ... | 2005 | 16100262 |
| e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects. | the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ... | 2005 | 16109942 |
| chromosomal stasis versus plasmid plasticity in aphid endosymbiont buchnera aphidicola. | the study of three genomes of the aphid endosymbiont buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. the reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first b. aphidicola analysed. the current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and ... | 2005 | 16118664 |
| variation in resistance to parasitism in aphids is due to symbionts not host genotype. | natural enemies are important ecological and evolutionary forces, and heritable variation in resistance to enemies is a prerequisite for adaptive responses of populations. such variation in resistance has been previously documented for pea aphids (acyrthosiphon pisum) attacked by the parasitoid wasp aphidius ervi. although the variation was presumed to reflect genotypic differences among the aphids, another potential source of resistance to a. ervi is infection by the facultative bacterial symbi ... | 2005 | 16120675 |
| new gammaproteobacteria associated with blood-feeding leeches and a broad phylogenetic analysis of leech endosymbionts. | many monophagous animals have coevolutionary relationships with bacteria that provide unavailable nutrients to the host. frequently, these microbial partners are vertically inherited and reside in specialized structures or tissues. here we report three new lineages of bacterial symbionts of blood-feeding leeches, one from the giant amazonian leech, haementeria ghilianii, and two others from placobdelloides species. these hosts each possess a different mycetome or esophageal organ morphology wher ... | 2005 | 16151107 |
| diversity in domain architectures of ser/thr kinases and their homologues in prokaryotes. | ser/thr/tyr kinases (styks) commonly found in eukaryotes have been recently reported in many bacterial species. recent studies elucidating their cellular functions have established their roles in bacterial growth and development. however functions of a large number of bacterial styks still remain elusive. the organisation of domains in a large dataset of bacterial styks has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial styks. | 2005 | 16171520 |
| mathematical design of prokaryotic clone-based microarrays. | clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. since the generation of a genomic dna library is a random process, it is beforehand uncertain which genes are represented. nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the li ... | 2005 | 16191193 |
| the players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes. | aphids maintain mutualistic symbioses involving consortia of coinherited organisms. all possess a primary endosymbiont, buchnera, which compensates for dietary deficiencies; many also contain secondary symbionts, such as hamiltonella defensa, which confers defense against natural enemies. genome sequences of uncultivable secondary symbionts have been refractory to analysis due to the difficulties of isolating adequate dna samples. by amplifying dna from hemolymph of infected pea aphids, we obtai ... | 2005 | 16195380 |
| genetic analysis identifies a function for the quec (ybax) gene product at an initial step in the queuosine biosynthetic pathway in escherichia coli. | queuosine (q), one of the most complex modifications occurring at the wobble position of trnas with gun anticodons, is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. despite these important implications, its biosynthetic pathway has remained unresolved. earlier, we observed that a naturally occurring strain of escherichia coli b105 lacked q modification in the trnas. in the present study, we developed a genetic screen to ... | 2005 | 16199558 |
| paenibacillus polymyxa invades plant roots and forms biofilms. | paenibacillus polymyxa is a plant growth-promoting rhizobacterium with a broad host range, but so far the use of this organism as a biocontrol agent has not been very efficient. in previous work we showed that this bacterium protects arabidopsis thaliana against pathogens and abiotic stress (s. timmusk and e. g. h. wagner, mol. plant-microbe interact. 12:951-959, 1999; s. timmusk, p. van west, n. a. r. gow, and e. g. h. wagner, p. 1-28, in mechanism of action of the plant growth promoting bacter ... | 2005 | 16269771 |
| preferential attachment in the evolution of metabolic networks. | many biological networks show some characteristics of scale-free networks. scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. in networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. here we have investigated preferential attachment in the context of metabolic networks. | 2005 | 16281983 |
| extracting single genomes from heterogenous dna samples: a test case with carsonella ruddii, the bacterial symbiont of psyllids (insecta). | analysis of many bacterial genomes is impeded by the inability to separate individual species from complex mixtures of cells or to propagate cells in pure culture. this problem is an obstacle to the study of many bacterial symbionts that live intracellularly in insects and other animals. to recover bacterial dna from complex samples, we devised a method that facilitates the cloning of dna fragments of distinctive g+c contents in order to generate shotgun dna libraries enriched in inserts having ... | 2005 | 16299593 |
| site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade. | site-2 proteases (s2ps) form a large family of membrane-embedded metalloproteases that participate in cellular signaling pathways through sequential cleavage of membrane-tethered substrates. using sequence similarity searches, we extend the s2p family to include remote homologs that help define a conserved structural core consisting of three predicted transmembrane helices with traditional metalloprotease functional motifs and a previously unrecognized motif (gxxxn/s/g). s2p relatives were ident ... | 2006 | 16322567 |
| symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum bacteroidetes. | several insect groups have obligate, vertically transmitted bacterial symbionts that provision hosts with nutrients that are limiting in the diet. some of these bacteria have been shown to descend from ancient infections. here we show that the large group of related insects including cicadas, leafhoppers, treehoppers, spittlebugs, and planthoppers host a distinct clade of bacterial symbionts. this newly described symbiont lineage belongs to the phylum bacteroidetes. analyses of 16s rrna genes in ... | 2005 | 16332876 |
| growth kinetics of the endosymbiont buchnera aphidicola in the aphid schizaphis graminum. | the aphid schizaphis graminum is dependent on its prokaryotic endosymbiont, buchnera aphidicola. as a means of determining b. aphidicola numbers during the growth cycle of the aphid we have used the quantitative pcr to measure the number of copies of rrs (the gene coding for 16s rrna, which is present as one copy in the b. aphidicola genome). in addition we have measured the aphid wet weight and the dna and protein content. the results indicate an approximately parallel (23- to 31-fold) increase ... | 1994 | 16349393 |
| occurrence of nitric oxide synthase in megoura viciae buckton (homoptera, aphididae): an histochemical and immunohistochemical localisation. | nitric oxide (no) is known to be involved in many physiological reactions of insects. we analysed nos localisation in aphids of the species megoura viciae by means of histochemical reaction for the nadph-diaphorase activity and immunohistochemical methods for unos, nnos and inos. the obtained data provided a complex and peculiar pattern of nos distribution in cells and tissue of m. viciae. the histochemical reaction for nadph-diaphorase was an indicative, but not exact marker of nos localisation ... | 2005 | 16377581 |
| plasmids in the aphid endosymbiont buchnera aphidicola with the smallest genomes. a puzzling evolutionary story. | buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. the most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a vari ... | 2006 | 16413149 |
| strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways. | a large majority of bacterial genomes show strand asymmetry, such that g and t preferentially accumulate on the leading strand. the mechanisms are unknown, but cytosine deaminations are thought to play an important role. here, we have examined dna strand asymmetry in three strains of the aphid endosymbiont buchnera aphidicola. these are phylogenetically related, have similar genomic gc contents, and conserved gene order structures, yet b. aphidicola (bp) shows a fourfold higher replication-induc ... | 2006 | 16476690 |
| compositional discordance between prokaryotic plasmids and host chromosomes. | most plasmids depend on the host replication machinery and possess partitioning genes. these properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. however, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, ... | 2006 | 16480495 |
| a dual-genome microarray for the pea aphid, acyrthosiphon pisum, and its obligate bacterial symbiont, buchnera aphidicola. | the best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont buchnera aphidicola. buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aphid and has co-speciated with its aphid hosts for the past 150 million years. we have used a single microarray to examine gene expression in the pea aphid, acyrthosiphon pisum, and its resident buchnera. very little is known of gene expression in aphids, few studies have examined gene exp ... | 2006 | 16536873 |
| costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures. | symbiosis is prevalent throughout the tree of life and has had a significant impact on the ecology and evolution of many bacteria and eukaryotes. the benevolence of symbiotic interactions often varies with the environment, and such variation is expected to play an important role in shaping the prevalence and distributions of symbiosis throughout nature. in this study, we examine how the fitness of aphids is influenced by infection with one of three maternally transmitted bacteria, 'candidatus se ... | 2006 | 16537132 |
| costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures. | symbiosis is prevalent throughout the tree of life and has had a significant impact on the ecology and evolution of many bacteria and eukaryotes. the benevolence of symbiotic interactions often varies with the environment, and such variation is expected to play an important role in shaping the prevalence and distributions of symbiosis throughout nature. in this study, we examine how the fitness of aphids is influenced by infection with one of three maternally transmitted bacteria, 'candidatus se ... | 2006 | 16537132 |
| chance and necessity in the evolution of minimal metabolic networks. | it is possible to infer aspects of an organism's lifestyle from its gene content. can the reverse also be done? here we consider this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. the diversity of gene content in these bacteria may reflect both variation in selective forces and contingency-dependent loss of alternative pathways. using an in silico representation of the metabolic network of escherichia coli, we examine the role of contingency by repeatedly simulat ... | 2006 | 16572170 |
| identification and localization of a rickettsia sp. in bemisia tabaci (homoptera: aleyrodidae). | whiteflies (homoptera: aleyrodidae) are sap-sucking insects that harbor "candidatus portiera aleyrodidarum," an obligatory symbiotic bacterium which is housed in a special organ called the bacteriome. these insects are also home for a diverse facultative microbial community which may include hamiltonella, arsenophonus, fritchea, wolbachia, and cardinium spp. in this study, the bacteria associated with a b biotype of the sweet potato whitefly bemisia tabaci were characterized using molecular fing ... | 2006 | 16672513 |
| outer membrane protein genes and their small non-coding rna regulator genes in photorhabdus luminescens. | three major outer membrane protein genes of escherichia coli, ompf, ompc, and ompa respond to stress factors. transcripts from these genes are regulated by the small non-coding rnas micf, micc, and mica, respectively. here we examine photorhabdus luminescens, an organism that has a different habitat from e. coli for outer membrane protein genes and their regulatory rna genes. | 2006 | 16716220 |
| costs and benefits of a superinfection of facultative symbionts in aphids. | symbiotic associations between animals and inherited micro-organisms are widespread in nature. in many cases, hosts may be superinfected with multiple inherited symbionts. acyrthosiphon pisum (the pea aphid) may harbour more than one facultative symbiont (called secondary symbionts) in addition to the obligate primary symbiont, buchnera aphidicola. previously we demonstrated that, in a controlled genetic background, a. pisum infected with either serratia symbiotica or hamiltonella defensa (calle ... | 2006 | 16720402 |
| metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. | mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. the symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. one such insect is the glassy-winged sharpshooter (homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. phylogenetic studies based on rrna have sh ... | 2006 | 16729848 |
| comparative rates of evolution in endosymbiotic nuclear genomes. | the nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. they also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they a ... | 2006 | 16772046 |
| who ate whom? adaptive helicobacter genomic changes that accompanied a host jump from early humans to large felines. | helicobacter pylori infection of humans is so old that its population genetic structure reflects that of ancient human migrations. a closely related species, helicobacter acinonychis, is specific for large felines, including cheetahs, lions, and tigers, whereas hosts more closely related to humans harbor more distantly related helicobacter species. this observation suggests a jump between host species. but who ate whom and when did it happen? in order to resolve this question, we determined the ... | 2006 | 16789826 |
| global transcriptome analysis of tropheryma whipplei in response to temperature stresses. | tropheryma whipplei, the agent responsible for whipple disease, is a poorly known pathogen suspected to have an environmental origin. the availability of the sequence of the 0.92-mb genome of this organism made a global gene expression analysis in response to thermal stresses feasible, which resulted in unique transcription profiles. a few genes were differentially transcribed after 15 min of exposure at 43 degrees c. the effects observed included up-regulation of the dnak regulon, which is comp ... | 2006 | 16816195 |
| tempo and mode of early gene loss in endosymbiotic bacteria from insects. | understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. in this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different buchnera aphidicola strains, wigglesworthia glossinidia, blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. we used a parsimony method to reconstruct a minimal ancestral genome of in ... | 2006 | 16848891 |
| analysis of nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation. | nanoarchaeum equitans, the only known hyperthermophilic archaeon exhibiting parasitic life style, has raised some new questions about the evolution of the archaea and provided a model of choice to study the genome landmarks correlated with thermo-parasitic adaptation. in this context, we have analyzed the genome and proteome composition of n. equitans and compared the same with those of other mesophiles, hyperthermophiles and obligatory host-associated organisms. | 2006 | 16869956 |
| activity of rhodobacter sphaeroides rpohii, a second member of the heat shock sigma factor family. | we have identified a second rpoh homolog, rpoh(ii), in the alpha-proteobacterium rhodobacter sphaeroides. primary amino acid sequence comparisons demonstrate that r. sphaeroides rpoh(ii) belongs to a phylogenetically distinct group with rpoh orthologs from alpha-proteobacteria that contain two rpoh genes. like its previously identified paralog, rpoh(i), rpoh(ii) is able to complement the temperature-sensitive phenotype of an escherichia coli sigma(32) (rpoh) mutant. in addition, we show that rec ... | 2006 | 16885439 |
| the emerging diversity of rickettsia. | the best-known members of the bacterial genus rickettsia are associates of blood-feeding arthropods that are pathogenic when transmitted to vertebrates. these species include the agents of acute human disease such as typhus and rocky mountain spotted fever. however, many other rickettsia have been uncovered in recent surveys of bacteria associated with arthropods and other invertebrates; the hosts of these bacteria have no relationship with vertebrates. it is therefore perhaps more appropriate t ... | 2006 | 16901827 |
| evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella. | the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ... | 2006 | 16923880 |
| genome rearrangements, deletions, and amplifications in the natural population of bartonella henselae. | cats are the natural host for bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. here, we have analyzed the natural variation in gene content and genome structure of 38 bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (pfge) blots. the variation in gene content was modest and confined to the prophage and the genomic islands, whereas the ... | 2006 | 16936024 |
| data mining for proteins characteristic of clades. | a synapomorphy is a phylogenetic character that provides evidence of shared descent. ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. with the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. we h ... | 2006 | 16936320 |
| hundreds of flagellar basal bodies cover the cell surface of the endosymbiotic bacterium buchnera aphidicola sp. strain aps. | buchnera aphidicola is the endosymbiotic bacterium of the pea aphid. due to its small genome size, buchnera lacks many essential genes for autogenous life but obtains nutrients from the host. although the buchnera cell is nonmotile, it retains clusters of flagellar genes that lack the late genes necessary for motility, including the flagellin gene. in this study, we show that the flagellar genes are actually transcribed and translated and that the buchnera cell surface is covered with hundreds o ... | 2006 | 16952945 |
| relevance of the endosymbiosis of blochmannia floridanus and carpenter ants at different stages of the life cycle of the host. | expression of several genes possibly involved in the symbiotic relationship between the obligate intracellular endosymbiont blochmannia floridanus and its ant host camponotus floridanus was investigated at different developmental stages of the host by real-time quantitative pcr. these included a set of genes related to nitrogen metabolism (urec, uref, glna, and speb) as well as genes involved in the synthesis of the aromatic amino acid tyrosine (tyra, aspc, and hisc). the overall transcriptional ... | 2006 | 16957225 |
| codon usage bias and trna over-expression in buchnera aphidicola after aromatic amino acid nutritional stress on its host acyrthosiphon pisum. | codon usage bias and relative abundances of trna isoacceptors were analysed in the obligate intracellular symbiotic bacterium, buchnera aphidicola from the aphid acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. codonusage in buchnera has been overcome by the high mutational bias towards at bases. however, several lines of evidence for c ... | 2006 | 16963497 |
| genome reduction in leptospira borgpetersenii reflects limited transmission potential. | leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. most infections are caused by either leptospira borgpetersenii or leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. we report the complete genomic sequences of two strains of l. borgpetersenii serovar hardjo that have distinct phenotypes and virulence. these two ... | 2006 | 16973745 |
| experimental and computational assessment of conditionally essential genes in escherichia coli. | genome-wide gene essentiality data sets are becoming available for escherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. here, we present an integrative model-driven analysis of the keio e. coli mutant collection screened in this study on glycerol-supplemented minimal medium. out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. these conditionally essential genes were then evaluated using a genome ... | 2006 | 17012394 |