| 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 |
| aphid thermal tolerance is governed by a point mutation in bacterial symbionts. | symbiosis is a ubiquitous phenomenon generating biological complexity, affecting adaptation, and expanding ecological capabilities. however, symbionts, which can be subject to genetic limitations such as clonality and genomic degradation, also impose constraints on hosts. a model of obligate symbiosis is that between aphids and the bacterium buchnera aphidicola, which supplies essential nutrients. we report a mutation in buchnera of the aphid acyrthosiphon pisum that recurs in laboratory lines a ... | 2007 | 17425405 |
| 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 |
| proteomic profiling of aphid macrosiphum euphorbiae responses to host-plant-mediated stress induced by defoliation and water deficit. | abiotic and biotic host-plant stress, such as desiccation and herbivory, may strongly affect sap-sucking insects such as aphids via changes in plant chemicals of insect nutritional or plant defensive value. here, we examined (i) water deprivation and (ii) defoliation by the beetle leptinotarsa decemlineata as stresses indirectly affecting the aphid macrosiphum euphorbiae via its host plant solanum tuberosum. for plant-induced stress, aphids were reared on healthy vs. continuously stressed potato ... | 2007 | 17466324 |
| 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 |
| 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 |
| 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 |
| rasta-bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes. | toxin/antitoxin (ta) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. we present rasta-bacteria, an automated method allowing quick and reliable identification of ta loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. the tool successfully confirmed all reported ta systems, and spotted new putative loci upon screening of sequenced genomes. rasta-bacteria i ... | 2007 | 17678530 |
| genome reduction in leptospira borgpetersenii reflects limited transmission potential. | leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. most infections are caused by either leptospira borgpetersenii or leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. we report the complete genomic sequences of two strains of l. borgpetersenii serovar hardjo that have distinct phenotypes and virulence. these two ... | 2006 | 16973745 |
| experimental and computational assessment of conditionally essential genes in escherichia coli. | genome-wide gene essentiality data sets are becoming available for escherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. here, we present an integrative model-driven analysis of the keio e. coli mutant collection screened in this study on glycerol-supplemented minimal medium. out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. these conditionally essential genes were then evaluated using a genome ... | 2006 | 17012394 |
| ftsz from divergent foreign bacteria can function for cell division in escherichia coli. | ftszs from mycoplasma pulmonis (mpuftsz) and bacillus subtilis (bsftsz) are only 46% and 53% identical in amino acid sequence to ftsz from escherichia coli (ecftsz). in the present study we show that mpuftsz and bsftsz can function for cell division in e. coli provided we make two modifications. first, we replaced their c-terminal tails with that from e. coli, giving the foreign ftsz the binding site for e. coli ftsa and zipa. second, we selected for mutations in the e. coli genome that facilita ... | 2006 | 17015652 |
| strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria. | host-symbiont cospeciation and reductive genome evolution have been identified in obligate endocellular insect symbionts, but no such example has been identified from extracellular ones. here we first report such a case in stinkbugs of the family plataspidae, wherein a specific gut bacterium is vertically transmitted via "symbiont capsule." in all of the plataspid species, females produced symbiont capsules upon oviposition and their gut exhibited specialized traits for capsule production. phylo ... | 2006 | 17032065 |
| a small microbial genome: the end of a long symbiotic relationship? | intracellular bacteria are characterized by genome reduction. the 422,434-base pair genome of buchnera aphidicola bcc, primary endosymbiont of the aphid cinara cedri, is approximately 200 kilobases smaller than the previously sequenced b. aphidicola genomes. b. aphidicola bcc has lost most metabolic functions, including the ability to synthesize the essential amino acid tryptophan and riboflavin. in addition, most retained genes are evolving rapidly. possibly, b. aphidicola bcc is losing its sym ... | 2006 | 17038625 |
| nutritional upgrading for omnivorous carpenter ants by the endosymbiont blochmannia. | carpenter ants (genus camponotus) are considered to be omnivores. nonetheless, the genome sequence of blochmannia floridanus, the obligate intracellular endosymbiont of camponotus floridanus, suggests a function in nutritional upgrading of host resources by the bacterium. thus, the strongly reduced genome of the endosymbiont retains genes for all subunits of a functional urease, as well as those for biosynthetic pathways for all but one (arginine) of the amino acids essential to the host. | 2007 | 17971224 |
| short-term temporal variability in airborne bacterial and fungal populations. | airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. as a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. cultivation-independent surveys of small-subunit rrna genes were conducted in order to identify the types ... | 2008 | 17981945 |
| short-term temporal variability in airborne bacterial and fungal populations. | airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. as a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. cultivation-independent surveys of small-subunit rrna genes were conducted in order to identify the types ... | 2008 | 17981945 |
| genomic resources for myzus persicae: est sequencing, snp identification, and microarray design. | the green peach aphid, myzus persicae (sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. however, despite the significant damage inflicted by m. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. | 2007 | 18021414 |
| molecular evolution of the h-ns protein: interaction with hha-like proteins is restricted to enterobacteriaceae. | we show here that chromosomal hha-like genes are restricted to the enterobacteriaceae. the h-ns n-terminal domain of members of this family includes an unaltered seven-amino-acid sequence located between helixes 1 and 2, termed the hha signature, that contains key residues for h-ns-hha interaction. | 2007 | 17041043 |
| genome reduction of the aphid endosymbiont buchnera aphidicola in a recent evolutionary time scale. | genome reduction, a typical feature of symbiotic bacteria, was analyzed in the last stages of evolution of buchnera aphidicola, the primary aphid endosymbiont, in two neutrally evolving regions: the pseudogene cmk and an intergenic region. these two regions were examined in endosymbionts from several lineages of their aphid host rhopalosiphum padi, and different species of the same genus, whose divergence times ranged from 0.62 to 19.51 million years. estimates of nucleotide substitution rates w ... | 2007 | 17098378 |
| molecular evolution of the h-ns protein: interaction with hha-like proteins is restricted to enterobacteriaceae. | we show here that chromosomal hha-like genes are restricted to the enterobacteriaceae. the h-ns n-terminal domain of members of this family includes an unaltered seven-amino-acid sequence located between helixes 1 and 2, termed the hha signature, that contains key residues for h-ns-hha interaction. | 2007 | 17041043 |
| the cyanobacterial endosymbiont of the unicellular algae rhopalodia gibba shows reductive genome evolution. | bacteria occur in facultative association and intracellular symbiosis with a diversity of eukaryotic hosts. recently, we have helped to characterise an intracellular nitrogen fixing bacterium, the so-called spheroid body, located within the diatom rhopalodia gibba. spheroid bodies are of cyanobacterial origin and exhibit features that suggest physiological adaptation to their intracellular life style. to investigate the genome modifications that have accompanied the process of endosymbiosis, her ... | 2008 | 18226230 |
| comparing patterns of natural selection across species using selective signatures. | comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. in the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and ... | 2008 | 18266472 |
| dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes. | reductive evolution in mitochondria and obligate intracellular microbes has led to a significant reduction in their genome size and guanine plus cytosine content (gc). we show that genome shrinkage during reductive evolution in prokaryotes follows an exponential decay pattern and provide a method to predict the extent of this decay on an evolutionary timescale. we validated predictions by comparison with estimated extents of genome reduction known to have occurred in mitochondria and buchnera ap ... | 2007 | 17108184 |
| high rate of mobilization for blactx-ms. | we constructed a phylogenetic analysis of class a beta-lactamases and found that the blactx-ms have been mobilized to plasmids approximately 10 times more frequently than other class a beta-lactamases. we also found that the blactx-ms are descended from a common ancestor that was incorporated in ancient times into the chromosome of the ancestor of kluyvera species through horizontal transfer. considerable sequence divergence has occurred among the descendents of that ancestral gene sequence sinc ... | 2008 | 18325257 |
| operon prediction for sequenced bacterial genomes without experimental information. | various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. in this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a bayesian hidden markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. the prediction algorithm performs as well ... | 2007 | 17122389 |
| how repetitive are genomes? | genome sequences vary strongly in their repetitiveness and the causes for this are still debated. here we propose a novel measure of genome repetitiveness, the index of repetitiveness, ir, which can be computed in time proportional to the length of the sequences analyzed. we apply it to 336 genomes from all three domains of life. | 2006 | 17187668 |
| selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes. | the evolutionary processes operating in the dna regions that participate in the regulation of gene expression are poorly understood. in escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. the density of promoter-like sequences, that could be recognizable by rna polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes ... | 2006 | 17096598 |
| a possible heterodimeric prophage-like element in the genome of the insect endosymbiont sodalis glossinidius. | extrachromosomal element psog3 (52,162 nucleotides) in the genome of sodalis glossinidius contains redundant phage-related gene pairs, indicating that it may have been formed by the fusion of two ancestral phage genomes followed by gene degradation. we suggest that psog3 is a prophage that has undergone genome degeneration accompanying host adaptation to symbiosis. | 2007 | 17209029 |
| reductive genome evolution from the mother of rickettsia. | the rickettsia genus is a group of obligate intracellular alpha-proteobacteria representing a paradigm of reductive evolution. here, we investigate the evolutionary processes that shaped the genomes of the genus. the reconstruction of ancestral genomes indicates that their last common ancestor contained more genes, but already possessed most traits associated with cellular parasitism. the differences in gene repertoires across modern rickettsia are mainly the result of differential gene losses f ... | 2007 | 17238289 |
| genome analysis of dna repair genes in the alpha proteobacterium caulobacter crescentus. | the integrity of dna molecules is fundamental for maintaining life. the dna repair proteins protect organisms against genetic damage, by removal of dna lesions or helping to tolerate them. dna repair genes are best known from the gamma-proteobacterium escherichia coli, which is the most understood bacterial model. however, genome sequencing raises questions regarding uniformity and ubiquity of these dna repair genes and pathways, reinforcing the need for identifying genes and proteins, which may ... | 2007 | 17352799 |
| stripped-down dna repair in a highly reduced parasite. | encephalitozoon cuniculi is a member of a distinctive group of single-celled parasitic eukaryotes called microsporidia, which are closely related to fungi. some of these organisms, including e. cuniculi, also have uniquely small genomes that are within the prokaryotic range. thus, e. cuniculi has undergone a massive genome reduction which has resulted in a loss of genes from diverse biological pathways, including those that act in dna repair.dna repair is essential to any living cell. a loss of ... | 2007 | 17374165 |
| on the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the common pathway genes. | the lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the common pathway (cp). in escherichia coli three different aspartokinases (aki, akii, akiii, the products of thra, metl and lysc, respectively) can perform the first step of the cp. moreover, two of them (aki and akii) are bifunctional, carrying also homoserine dehydrogenasic activity (hom product). the second step of the cp is catalyzed by a single aspartate semialdehy ... | 2007 | 17430556 |
| modular organization in the reductive evolution of protein-protein interaction networks. | the variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. the organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. high-throughput protein interaction data now make it possible to examine the additional complexity generated by the way that protein interactions are organized. | 2007 | 17532860 |
| the striking case of tryptophan provision in the cedar aphid cinara cedri. | buchnera aphidicola bcc has lost its symbiotic role as the tryptophan supplier to the aphid cinara cedri. we report the presence of a plasmid in this endosymbiont that contains the trpeg genes. the remaining genes for the pathway (trpdcba) are located on the chromosome of the secondary endosymbiont "candidatus serratia symbiotica." thus, we propose that a symbiotic consortium is necessary to provide tryptophan. | 2008 | 18586942 |
| toxic introns and parasitic intein in coxiella burnetii: legacies of a promiscuous past. | the genome of the obligate intracellular pathogen coxiella burnetii contains a large number of selfish genetic elements, including two group i introns (cbu.l1917 and cbu.l1951) and an intervening sequence that interrupts the 23s rrna gene, an intein (cbu.dnab) within dnab and 29 insertion sequences. here, we describe the ability of the intron-encoded rnas (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of cbu.dnab. when expressed in e ... | 2008 | 18606739 |
| genetic evidence from mitochondrial, nuclear, and endosymbiont markers for the evolution of host plant associated species in the aphid genus hyalopterus (hemiptera: aphididae). | over the past several decades biologists' fascination with plant-herbivore interactions has generated intensive research into the implications of these interactions for insect diversification. the study of closely related phytophagous insect species or populations from an evolutionary perspective can help illuminate ecological and selective forces that drive these interactions. here we present such an analysis for aphids in the genus hyalopterus (hemiptera: aphididae), a cosmopolitan group that ... | 2007 | 17542845 |
| conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of buchnera aphidicola. | genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. we have explored the possible conservation of relationships between mrna abundances and chromosomal organization in the highly reduced genome of buchnera aphidicola, the primary ... | 2007 | 17547756 |
| an insecticidal groel protein with chitin binding activity from xenorhabdus nematophila. | xenorhabdus nematophila secretes insecticidal proteins to kill its larval prey. we have isolated an approximately 58-kda groel homolog, secreted in the culture medium through outer membrane vesicles. the protein was orally insecticidal to the major crop pest helicoverpa armigera with an lc50 of approximately 3.6 microg/g diet. for optimal insecticidal activity all three domains of the protein, apical, intermediate, and equatorial, were necessary. the apical domain alone was able to bind to the l ... | 2008 | 18667427 |
| obligate symbiont involved in pest status of host insect. | the origin of specific insect genotypes that enable efficient use of agricultural plants is an important subject not only in applied fields like pest control and management but also in basic disciplines like evolutionary biology. conventionally, it has been presupposed that such pest-related ecological traits are attributed to genes encoded in the insect genomes. here, however, we report that pest status of an insect is principally determined by symbiont genotype rather than by insect genotype. ... | 2007 | 17567556 |
| reconstructing the ancestor of mycobacterium leprae: the dynamics of gene loss and genome reduction. | we have reconstructed the gene content and order of the last common ancestor of the human pathogens mycobacterium leprae and mycobacterium tuberculosis. during the reductive evolution of m. leprae, 1537 of 2977 ancestral genes were lost, among which we found 177 previously unnoticed pseudogenes. we find evidence that a massive gene inactivation took place very recently in the m. leprae lineage, leading to the loss of hundreds of ancestral genes. a large proportion of their nucleotide content ( a ... | 2007 | 17623808 |
| the insecticidal activity of recombinant garlic lectins towards aphids. | the heterodimeric and homodimeric garlic lectins asai and asaii were produced as recombinant proteins in the yeast pichia pastoris. the proteins were purified as functional dimeric lectins, but underwent post-translational proteolysis. recombinant asaii was a single homogenous polypeptide which had undergone c-terminal processing similar to that occurring in planta. the recombinant asai was glycosylated and subject to variable and heterogenous proteolysis. both lectins showed insecticidal effect ... | 2008 | 18707000 |
| comparative phylogenomics and multi-gene cluster analyses of the citrus huanglongbing (hlb)-associated bacterium candidatus liberibacter. | huanglongbing (hlb, previously known as citrus greening), is associated with candidatus liberibacter species and is a serious threat to citrus production world-wide. the pathogen is a gram negative, unculturable, phloem-limited bacterium with limited known genomic information. expanding the genetic knowledge of this organism may provide better understanding of the pathogen and possibly develop effective strategies for control and management of hlb. | 2008 | 18755041 |
| gene promoter scan methodology for identifying and classifying coregulated promoters. | a critical challenge of the postgenomic era is to understand how genes are differentially regulated. genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks in both prokaryotes and eukaryotes. however, little is known about what determines the differential expression of genes within a particular network, even when it involves a single transcription factor. the fact that coregulated genes may be differentially expressed suggests that subtle diffe ... | 2007 | 17628149 |
| bacterial endosymbiont of the slender pigeon louse, columbicola columbae, allied to endosymbionts of grain weevils and tsetse flies. | the current study focuses on a symbiotic bacterium found in the slender pigeon louse, columbicola columbae (insecta: phthiraptera). molecular phylogenetic analyses indicated that the symbiont belongs to the gamma subdivision of the class proteobacteria and is allied to sodalis glossinidius, the secondary symbiont of tsetse flies (glossina spp.) and also to the primary symbiont of grain weevils (sitophilus spp.). relative-rate tests revealed that the symbiont of c. columbae exhibits accelerated m ... | 2007 | 17766458 |
| the role of mutational dynamics in genome shrinkage. | genome shrinkage occurs after whole genome duplications (wgds) and in the evolution of parasitic or symbiotic species. the dynamics of this process, whether it occurs by single gene deletions or also by larger deletions are however unknown. in yeast, genome shrinkage has occurred after a wgd. using a computational model of genome evolution, we show that in a random genome single gene deletions cannot explain the observed pattern of gene loss in yeast. the distribution of genes deleted per event ... | 2007 | 17768305 |
| the frontier between cell and organelle: genome analysis of candidatus carsonella ruddii. | bacterial symbioses are widespread among insects. the early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new imbalanced food resources, such as plant sap or blood. several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. recently, the complete genome sequence ... | 2007 | 17908294 |
| analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus mannheimia. | the mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. for example, m. haemolytica + m. glucosida are potential pathogens of the respiratory tract in the mammalian suborder ruminantia, whereas m. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. we have tested the hypothesis that vertical inheritance of the leukotoxin (lktcabd) operon has occurred from the last common ancestor of genus mannheimia ... | 2007 | 17915007 |
| lateral gene transfer between obligate intracellular bacteria: evidence from the rickettsia massiliae genome. | rickettsia massiliae is a tick-borne obligate intracellular alpha-proteobacteria causing spotted fever in humans. here, we present the sequence of its genome, comprising a 1.3-mb circular chromosome and a 15.3-kb plasmid. the chromosome exhibits long-range colinearity with the other spotted fever group rickettsia genomes, except for a large fragment specific to r. massiliae that contains 14 tra genes presumably involved in pilus formation and conjugal dna transfer. we demonstrate that the tra re ... | 2007 | 17916642 |
| parallel genomic evolution and metabolic interdependence in an ancient symbiosis. | obligate symbioses with nutrient-provisioning bacteria have originated often during animal evolution and have been key to the ecological diversification of many invertebrate groups. to date, genome sequences of insect nutritional symbionts have been restricted to a related cluster within gammaproteobacteria and have revealed distinctive features, including extreme reduction, rapid evolution, and biased nucleotide composition. using recently developed sequencing technologies, we show that sulcia ... | 2007 | 18048332 |
| chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race. | the genomes of pathogens are thought to have evolved under selective pressure provided by the host in a coevolutionary arms race (the 'red queen's hypothesis'). traditionally, adaptation by pathogens is thought to rely not on whole chromosome dynamics but on gain/loss of specific genes, yielding differential abilities to infect distinct tissues. thus, it is not known whether distinct host organs differently shape the genome of the same pathogen. we tested this hypothesis using chlamydia trachoma ... | 2008 | 18947394 |
| using mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. | plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. to understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. since extensive data support the proposal that foreign dna acquires the host's nucleotide composition during long-term residence, comparison of nucleotide ... | 2008 | 18953039 |
| a genomic distance based on mum indicates discontinuity between most bacterial species and genera. | the fundamental unit of biological diversity is the species. however, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ani), which detects the dna conservation of the core genome, and the dna content, which calculates the proportion of dna share ... | 2009 | 18978054 |
| a genomic distance based on mum indicates discontinuity between most bacterial species and genera. | the fundamental unit of biological diversity is the species. however, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ani), which detects the dna conservation of the core genome, and the dna content, which calculates the proportion of dna share ... | 2009 | 18978054 |
| impact of plant nutrients on the relationship between a herbivorous insect and its symbiotic bacteria. | the interactions between herbivorous insects and their symbiotic micro-organisms can be influenced by the plant species on which the insects are reared, but the underlying mechanisms are not understood. here, we identify plant nutrients, specifically amino acids, as a candidate factor affecting the impact of symbiotic bacteria on the performance of the phloem-feeding aphid aphis fabae. aphis fabae grew more slowly on the labiate plant lamium purpureum than on an alternative host plant vicia faba ... | 2008 | 18089538 |
| impact of plant nutrients on the relationship between a herbivorous insect and its symbiotic bacteria. | the interactions between herbivorous insects and their symbiotic micro-organisms can be influenced by the plant species on which the insects are reared, but the underlying mechanisms are not understood. here, we identify plant nutrients, specifically amino acids, as a candidate factor affecting the impact of symbiotic bacteria on the performance of the phloem-feeding aphid aphis fabae. aphis fabae grew more slowly on the labiate plant lamium purpureum than on an alternative host plant vicia faba ... | 2008 | 18089538 |
| symbiotic bacteria enable insect to use a nutritionally inadequate diet. | animals generally require a dietary supply of various nutrients (vitamins, essential amino acids, etc.) because their biosynthetic capabilities are limited. the capacity of aphids to use plant phloem sap, with low essential amino acid content, has been attributed to their symbiotic bacteria, buchnera aphidicola, which can synthesize these nutrients; but this has not been demonstrated empirically. we demonstrate here that phloem sap obtained from the severed stylets of pea aphids acyrthosiphon pi ... | 2009 | 19129128 |
| symbiotic bacteria enable insect to use a nutritionally inadequate diet. | animals generally require a dietary supply of various nutrients (vitamins, essential amino acids, etc.) because their biosynthetic capabilities are limited. the capacity of aphids to use plant phloem sap, with low essential amino acid content, has been attributed to their symbiotic bacteria, buchnera aphidicola, which can synthesize these nutrients; but this has not been demonstrated empirically. we demonstrate here that phloem sap obtained from the severed stylets of pea aphids acyrthosiphon pi ... | 2009 | 19129128 |
| different levels of transcriptional regulation due to trophic constraints in the reduced genome of buchnera aphidicola aps. | symbiotic associations involving intracellular microorganisms and animals are widespread, especially for species feeding on poor or unbalanced diets. buchnera aphidicola, the obligate intracellular bacterium associated with most aphid species, provides its hosts with essential amino acids (eaas), nutrients in short supply in the plant phloem sap. the buchnera genome has undergone severe reductions during intracellular evolution. genes for eaa biosynthesis are conserved, but most of the transcrip ... | 2006 | 17041159 |
| the dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. | among cellular organisms, symbiotic bacteria provide the extreme examples of genome degradation and reduction. however, only isolated snapshots of eroding symbiont genomes have previously been available. we documented the dynamics of symbiont genome evolution by sequencing seven strains of buchnera aphidicola from pea aphid hosts. we estimated a spontaneous mutation rate of at least 4 x 10(-9) substitutions per site per replication, which is more than 10 times as high as the rates previously est ... | 2009 | 19150844 |
| codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in lawsonia intracellularis. | in this study, the factors driving genome-wide patterns of codon usages in lawsonia intracellularis genome are determined. for genes on the chromosome of the bacterium, it is found that the most important source of variation results from strand-specific mutational biases. a lesser trend of variation is attributable to genes that are presumed as horizontally transferred. these putative alien genes are unusually gc richer than the other genes, whereas horizontally transferred genes have been obser ... | 2009 | 19221094 |
| a fragile metabolic network adapted for cooperation in the symbiotic bacterium buchnera aphidicola. | in silico analyses provide valuable insight into the biology of obligately intracellular pathogens and symbionts with small genomes. there is a particular opportunity to apply systems-level tools developed for the model bacterium escherichia coli to study the evolution and function of symbiotic bacteria which are metabolically specialised to overproduce specific nutrients for their host and, remarkably, have a gene complement that is a subset of the e. coli genome. | 2009 | 19232131 |
| reducing the false positive rate in the non-parametric analysis of molecular coevolution. | the strength of selective constraints operating on amino acid sites of proteins has a multifactorial nature. in fact, amino acid sites within proteins coevolve due to their functional and/or structural relationships. different methods have been developed that attempt to account for the evolutionary dependencies between amino acid sites. researchers have invested a significant effort to increase the sensitivity of such methods. however, the difficulty in disentangling functional co-dependencies f ... | 2008 | 18402697 |
| structure and biological function of the rna pyrophosphohydrolase bdrpph from bdellovibrio bacteriovorus. | until recently, the mechanism of mrna decay in bacteria was thought to be different from that of eukaryotes. this paradigm changed with the discovery that rpph (orf176/nudh/ygdp), an escherichia coli enzyme that belongs to the nudix superfamily, is an rna pyrophosphohydrolase that initiates mrna decay by cleaving pyrophosphate from the 5'-triphosphate. here we report the 1.9 angstroms resolution structure of the nudix hydrolase bdrpph from bdellovibrio bacteriovorus, a bacterium that feeds on ot ... | 2009 | 19278661 |
| aphids acquired symbiotic genes via lateral gene transfer. | aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist buchnera aphidicola (gamma-proteobacteria). buchnera has lost many of the genes that appear to be essential for bacterial life. from the bacteriocyte of the pea aphid acyrthosiphon pisum, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. southern blot analysis demonstrated that they are encoded in the aphid genome. in this stu ... | 2009 | 19284544 |
| global distribution and evolution of a toxinogenic burkholderia-rhizopus symbiosis. | toxinogenic endobacteria were isolated from a collection of rhizopus spp. representing highly diverse geographic origins and ecological niches. all endosymbionts belonged to the burkholderia rhizoxinica complex according to matrix-assisted laser desorption ionization-time of flight biotyping and multilocus sequence typing, suggesting a common ancestor. comparison of host and symbiont phylogenies provides insights into possible cospeciation and horizontal-transmission events. | 2009 | 19286793 |
| extreme polyploidy in a large bacterium. | cells rely on diffusion to move metabolites and biomolecules. diffusion is highly efficient but only over short distances. although eukaryotic cells have broken free of diffusion-dictated constraints on cell size, most bacteria and archaea are forced to remain small. exceptions to this rule are found among the bacterial symbionts of surgeonfish; epulopiscium spp. are cigar-shaped cells that reach lengths in excess of 600 mum. a large epulopiscium contains thousands of times more dna than a bacte ... | 2008 | 18445653 |
| in silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles. | in silico candidate gene prioritisation (cgp) aids the discovery of gene functions by ranking genes according to an objective relevance score. while several cgp methods have been described for identifying human disease genes, corresponding methods for prokaryotic gene function discovery are lacking. here we present two prokaryotic cgp methods, based on phylogenetic profiles, to assist with this task. | 2009 | 19292914 |
| infection dynamics of coexisting beta- and gammaproteobacteria in the nested endosymbiotic system of mealybugs. | we investigated the infection dynamics of endosymbiotic bacteria in the developmental course of the mealybugs planococcus kraunhiae and pseudococcus comstocki. molecular phylogenetic analyses identified a betaproteobacterium and a gammaproteobacterium from each of the mealybug species. the former bacterium was related to the beta-endosymbionts of other mealybugs, i.e., "candidatus tremblaya princeps," and formed a compact clade in the betaproteobacteria. meanwhile, the latter bacterium was relat ... | 2008 | 18469124 |
| triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. | bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. this difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. | 2008 | 18471287 |
| interactions of chaperonin with a weakly active anthranilate synthase from the aphid endosymbiont buchnera aphidicola. | the endosymbiotic bacterium buchnera provides its aphid host with essential amino acids. buchnera is typical of intracellular symbiotic and parasitic microorganisms in having a small effective population size, which is believed to accelerate genetic drift and reduce the stability of gene products. it is hypothesized that buchnera mitigates protein instability with an increased production of the chaperonins groesl. in this paper, we report the expression and functional analysis of trpe, a plasmid ... | 2008 | 18478288 |
| evolution of the secondary symbiont "candidatus serratia symbiotica" in aphid species of the subfamily lachninae. | buchnera aphidicola bcc, the primary endosymbiont of the aphid cinara cedri (subfamily lachninae), is losing its symbiotic capacity and might be replaced by the coresident "candidatus serratia symbiotica." phylogenetic and morphological analyses within the subfamily lachninae indicate two different "ca. serratia symbiotica" lineages and support the longtime coevolution of both symbionts in c. cedri. | 2008 | 18502932 |
| patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of ants blochmannia floridanus. | genome reduction is a general process that has been studied in numerous symbiotic bacteria associated with insects. we investigated the last stages of genome degradation in blochmannia floridanus, a mutualistic bacterial endosymbiont of the ant camponotus floridanus. we determined the tempo (rates of insertion and deletion) and mode (size and number of insertion-deletion events) of the process in the last 200,000 years by analysing a total of 16 intergenic regions in several strains of this endo ... | 2008 | 19378410 |
| biosynthetic potentials from species-specific metabolic networks. | studies of genome-scale metabolic networks allow for qualitative and quantitative descriptions of an organism's capability to convert nutrients into products. the set of synthesizable products strongly depends on the provided nutrients as well as on the structure of the metabolic network. here, we apply the method of network expansion and the concept of scopes, describing the synthesizing capacities of an organism when certain nutrients are provided. we analyze the biosynthetic properties of fou ... | 2008 | 19425129 |
| go4genome: a prokaryotic phylogeny based on genome organization. | determining the phylogeny of closely related prokaryotes may fail in an analysis of rrna or a small set of sequences. whole-genome phylogeny utilizes the maximally available sample space. for a precise determination of genome similarity, two aspects have to be considered when developing an algorithm of whole-genome phylogeny: (1) gene order conservation is a more precise signal than gene content; and (2) when using sequence similarity, failures in identifying orthologues or the in situ replaceme ... | 2009 | 19436929 |
| edgar: a software framework for the comparative analysis of prokaryotic genomes. | the introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. as one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. a main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. | 2009 | 19457249 |
| comparative genomics of the inca/c multidrug resistance plasmid family. | multidrug resistance (mdr) plasmids belonging to the inca/c plasmid family are widely distributed among salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant yersinia pestis isolate (ip275) from madagascar. here, we present the complete plasmid sequences of the inca/c reference plasmid pra1 (143,963 bp), isolated in 1971 from the fish pathogen aeromonas hydrophila, and of the cryptic inca/c plasmid prax (49,763 b ... | 2009 | 19482926 |
| fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification. | the sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 x 10(6) to 3.0 x 10(7) bp from archaea, bacteria, arabidopsis thaliana, saccharomyces cerevisiae, schizosaccharomyces po ... | 2009 | 19533117 |
| ests from the microsporidian edhazardia aedis. | microsporidia are a group of parasites related to fungi that infect a wide variety of animals and have gained recognition from the medical community in the past 20 years due to their ability to infect immuno-compromised humans. microsporidian genomes range in size from 2.3 to 19.5 mbp, but almost all of our knowledge comes from species that have small genomes (primarily from the human parasite encephalitozoon cuniculi and the locust parasite antonospora locustae). we have conducted an est survey ... | 2008 | 18570666 |
| borrelia burgdorferi vlse antigenic variation is not mediated by reca. | reca is a key protein linking genetic recombination to dna replication and repair in bacteria. previous functional characterization of borrelia burgdorferi reca indicated that the protein is mainly involved in genetic recombination rather than dna repair. genetic recombination may play a role in b. burgdorferi persistence by generation of antigenic variation. we report here the isolation of a reca null mutant in an infectious b. burgdorferi strain. comparison of the in vitro growth characteristi ... | 2008 | 18606826 |
| tuberculosis vaccine strain mycobacterium bovis bcg russia is a natural reca mutant. | the current tuberculosis vaccine is a live vaccine derived from mycobacterium bovis and attenuated by serial in vitro passaging. all vaccine substrains in use stem from one source, strain bacille calmette-guérin. however, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. | 2008 | 18637199 |
| complete rpob gene sequencing as a suitable supplement to dna-dna hybridization for bacterial species and genus delineation. | dna-dna hybridization (ddh), the gold standard for bacterial species delineation, is a laborious method and the alternative, average nucleotide identity (ani), a genomic sequence-derived parameter, is not applicable to non-sequenced species. a universal cut-off value to delineate bacterial species does not exist, yet a ddh value <70 % and ani <95+/-0.5 % have proved useful in selected examples. we herein compare published values for ddh and ani with sequence similarity of rpob gene sequences ret ... | 2008 | 18676461 |
| the obligate mutualist wigglesworthia glossinidia influences reproduction, digestion, and immunity processes of its host, the tsetse fly. | tsetse flies (diptera: glossinidae) are vectors for trypanosome parasites, the agents of the deadly sleeping sickness disease in africa. tsetse also harbor two maternally transmitted enteric mutualist endosymbionts: the primary intracellular obligate wigglesworthia glossinidia and the secondary commensal sodalis glossinidius. both endosymbionts are transmitted to the intrauterine progeny through the milk gland secretions of the viviparous female. we administered various antibiotics either contin ... | 2008 | 18689507 |
| whole-genome analyses reveal genetic instability of acetobacter pasteurianus. | acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. to clarify the mutability, acetobacter pasteurianus nbrc 3283, which forms a multi-phenotype cell complex, was subjected to genome dna sequencing. the genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-mb chromosome and six plasmids. there were three single nucleotide muta ... | 2009 | 19638423 |
| fine-scale cospeciation between brachycaudus and buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids. | aphids harbour an obligatory symbiont, buchnera aphidicola, providing essential amino acids not supplied by their diet. these bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. we investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus brachycaudus. we used dna-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and buchnera species and to infer asso ... | 2009 | 18782748 |
| implications of high level pseudogene transcription in mycobacterium leprae. | the mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. preliminary evidence suggests that some pseudogenes are expressed. therefore, defining pseudogene transcriptional and translational potentials of this genome should increase our understanding of their impact on m. leprae physiology. | 2009 | 19706172 |
| fine-scale cospeciation between brachycaudus and buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids. | aphids harbour an obligatory symbiont, buchnera aphidicola, providing essential amino acids not supplied by their diet. these bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. we investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus brachycaudus. we used dna-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and buchnera species and to infer asso ... | 2009 | 18782748 |
| facultative symbionts in aphids and the horizontal transfer of ecologically important traits. | aphids engage in symbiotic associations with a diverse assemblage of heritable bacteria. in addition to their obligate nutrient-provisioning symbiont, buchnera aphidicola, aphids may also carry one or more facultative symbionts. unlike obligate symbionts, facultative symbionts are not generally required for survival or reproduction and can invade novel hosts, based on both phylogenetic analyses and transfection experiments. facultative symbionts are mutualistic in the context of various ecologic ... | 2010 | 19728837 |
| prevalence of cardinium bacteria in planthoppers and spider mites and taxonomic revision of "candidatus cardinium hertigii" based on detection of a new cardinium group from biting midges. | cardinium bacteria, members of the phylum cytophaga-flavobacterium-bacteroides (cfb), are intracellular bacteria in arthropods that are capable of inducing reproductive abnormalities in their hosts, which include parasitic wasps, mites, and spiders. a high frequency of cardinium infection was detected in planthoppers (27 out of 57 species were infected). a high frequency of cardinium infection was also found in spider mites (9 out of 22 species were infected). frequencies of double infection by ... | 2009 | 19734338 |
| endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(a) tracts. | among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160-790 kb) and most a + t-rich (>70%) bacterial genomes known to date. these genomes are riddled with poly(a) tracts, and 5-50% of genes contain tracts of 10 as or more. here, we demonstrate transcriptional slippage at poly(a) tracts within genes of buchnera aphidicola associated with aphids and blochmannia pennsylvanicus associated with ants. se ... | 2008 | 18815381 |
| suppression of deltabipa phenotypes in escherichia coli by abolishment of pseudouridylation at specific sites on the 23s rrna. | the bipa protein of escherichia coli has intriguing similarities to the elongation factor subfamily of gtpases, including ef-tu, ef-g, and lepa. in addition, phenotypes of a bipa deletion mutant suggest that bipa is involved in regulation of a variety of pathways. these two points have led to speculation that bipa may be a novel regulatory protein that affects efficient translation of target genes through direct interaction with the ribosome. we isolated and characterized suppressors of the cold ... | 2008 | 18820021 |
| bioinformatics identification of murj (mvin) as the peptidoglycan lipid ii flippase in escherichia coli. | peptidoglycan is a cell-wall glycopeptide polymer that protects bacteria from osmotic lysis. whereas in gram-positive bacteria it also serves as scaffold for many virulence factors, in gram-negative bacteria, peptidoglycan is an anchor for the outer membrane. for years, we have known the enzymes required for the biosynthesis of peptidoglycan; what was missing was the flippase that translocates the lipid-anchored precursors across the cytoplasmic membrane before their polymerization into mature p ... | 2008 | 18832143 |
| impact of host developmental age on the transcriptome of the symbiotic bacterium buchnera aphidicola in the pea aphid (acyrthosiphon pisum). | of the 617 genes from buchnera aphidicola, the obligate bacterial symbiont of the pea aphid, 23% were differentially expressed in embryos compared to adults. genes involved in flagellar apparatus and riboflavin synthesis exhibited particularly robust upregulation in embryos, suggesting functional differences between the symbiosis in the adult and embryo insect. | 2009 | 19783752 |
| accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria. | despite a large agreement between ribosomal rna and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. for instance, the position of the hyperthermophilic aquificales is debated, as their commonly observed position close to thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. indeed, another view, based on the analysis of rare genomic c ... | 2008 | 18834516 |
| post-pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts. | adaptation to different resources has the potential to cause rapid species diversification, but few studies have been able to quantify the time scale of recent adaptive radiations. the pea aphid, acyrthosiphon pisum, a model of speciation for host-specialized parasites, consists of several biotypes (races or species) living on distinct legume hosts. to document this radiation, we used rapidly evolving sequences from buchnera, the maternally transmitted bacterial endosymbiont of aphids. analyses ... | 2009 | 19805299 |
| integrated metabonomic-proteomic analysis of an insect-bacterial symbiotic system. | the health of animals, including humans, is dependent on their resident microbiota, but the complexity of the microbial communities makes these associations difficult to study in most animals. exceptionally, the microbiology of the pea aphid acyrthosiphon pisum is dominated by a single bacterium buchnera aphidicola (b. aphidicola). a (1)h nmr-based metabonomic strategy was applied to investigate metabolic profiles of aphids fed on a low essential amino acid diet and treated by antibiotic to elim ... | 2010 | 19860485 |
| preferred and avoided codon pairs in three domains of life. | alternative synonymous codons are not used with equal frequencies. in addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. the codon context can influence both translational accuracy and elongation rates. however, it is not known how strong or conserved the codon context preferences in different organisms are. we analyzed 138 organisms (bacteria, archaea and eukaryotes) to find conserved patterns of codon pairs. | 2008 | 18842120 |