Publications

diversity and geographic distribution of secondary endosymbiotic bacteria in natural populations of the pea aphid, acyrthosiphon pisum.	in addition to the essential intracellular symbiotic bacterium buchnera, several facultative endosymbiotic bacteria called collectively secondary symbionts (s-symbionts) have been identified from the pea aphid acyrthosiphon pisum. we conducted an extensive and systematic survey of s-symbionts in japanese local populations of a. pisum using a specific pcr detection technique. five s-symbionts of a. pisum, pass, paus, pabs, rickettsia and spiroplasma, and two facultative endosymbionts universally ...	2002	12296954
molecular characterization of the leucine cluster in buchnera sp. strain psy, a primary endosymbiont of the aphid pemphigus spyrothecae.	buchnera strains from most aphid subfamilies studied to date have been found to carry the leucine gene cluster (leua, -b, -c, and -d) on a plasmid, an organization unique among bacteria. here, however, we demonstrate a classical chromosomal location of the cluster in buchnera sp. strain psy from the aphid pemphigus spyrothecae (subfamily pemphiginae). the genes that flank leuabcd in buchnera sp. strain psy appear to be adjacent in the genome of buchnera sp. strain aps, a strain carrying a leucin ...	2002	11976137
comparative genomics of microbial pathogens and symbionts.	we are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. a particular focus is on intracellular pathogens and symbionts of the genera rickettsia, bartonella and buchnera: extensive gene loss and restricted access to phage and plasmid pools may ...	2002	12385978
genome evolution in bacterial endosymbionts of insects.	many insect species rely on intracellular bacterial symbionts for their viability and fecundity. large-scale dna-sequence analyses are revealing the forces that shape the evolution of these bacterial associates and the genetic basis of their specialization to an intracellular lifestyle. the full genome sequences of two obligate mutualists, buchnera aphidicola of aphids and wigglesworthia glossinidia of tsetse flies, reveal substantial gene loss and an integration of host and symbiont metabolic f ...	2002	12415315
extremely low levels of genetic polymorphism in endosymbionts (buchnera) of aphids (pemphigus).	molecular evolutionary studies have suggested that vertically transmitted endosymbionts are subject to accumulation of deleterious mutations through genetic drift. predictions of this hypothesis for patterns of intraspecific polymorphism were borne out in the single relevant study available, on the symbiont buchnera aphidicola of uroleucon ambrosiae. in order to examine the generality of this result, we surveyed dna sequence variation in buchnera of the distantly related aphid, pemphigus obesiny ...	2002	12453247
[cloning and prokaryotic expression of viral binding protein(vbp) gene from endosybiotic bacterium of rhopalosiphum padi].	viral binding protein gene from rhopalosiphum padi yangling biotype was amplified by pcr method and then cloned. the complete nucleotide sequence of the gene was determined, it has 1647 nucleotides encoding 548 amino acids. comparison showed this gene has 97% identity on nucleotide level with buchnera groel-am gene of rhopalosiphum padi american biotype, while has 97.4% identity on amino acid level was found between this two genes. the vbp gene was ligated into pbv221 and pet30a expression vecto ...	2002	12557551
metabolic and symbiotic interactions in amino acid pools of the pea aphid, acyrthosiphon pisum, parasitized by the braconid aphidius ervi.	aphidius ervi haliday (hymenoptera, braconidae) is an endophagous parasitoid of the pea aphid, acyrthosiphon pisum (harris) (homoptera, aphididae). this parasitoid strongly redirects host reproduction and metabolism to favour nutrition and development of its juvenile stages. parasite-regulated biosynthesis and mobilization of nitrogen metabolites determine a significant increase of host nutritional suitability. the aim of the present study was mainly to investigate the temporal changes of a. pis ...	2002	12770078
an experimental validation of orphan genes of buchnera, a symbiont of aphids.	although buchnera sp. aps, an intracellular symbiont of pea aphids, is a close relative of escherichia coli, its genome has been extensively modified because of its prolonged intracellular life. in our previous studies on the buchnera genome, computer analysis predicted three "orphan" genes, yba2, yba3, and yba4, which are open reading frames (orfs) with no homologs in the database. in this paper, we successfully validated all these orphan genes by rt-pcr and northern hybridization. the present ...	2002	11890702
extreme genome reduction in buchnera spp.: toward the minimal genome needed for symbiotic life.	buchnera is a mutualistic intracellular symbiont of aphids. their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. during this coevolutionary process, buchnera has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. previous studies reported that genome size in buchnera spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lin ...	2002	11904373
the evolution of the heat-shock protein groel from buchnera, the primary endosymbiont of aphids, is governed by positive selection.	the heat-shock protein groel is a double-ring-structured chaperonin that assists the folding of many newly synthesized proteins in escherichia coli and the refolding in vitro, with the cochaperonin groes, of conformationally damaged proteins. this protein is constitutively overexpressed in the primary symbiotic bacteria of many insects, constituting approximately 10% of the total protein in buchnera, the primary endosymbiont of aphids. in the present study, we perform a maximum likelihood (ml) a ...	2002	12082135
estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria.	many species of bacterial endosymbionts are acquired by animal hosts before birth, through direct transmission from mothers to eggs or embryos. this vertical transmission imposes a reduction in numbers or "bottleneck," and the size of this bottleneck affects the population structure and evolution of symbiotic lineages. we have estimated the size of the transmission bottleneck in buchnera, the bacterial symbiont of aphids, using basic light and electron microscopy techniques. by serial-sectioning ...	2002	12087426
the genetic properties of the primary endosymbionts of mealybugs differ from those of other endosymbionts of plant sap-sucking insects.	mealybugs (hemiptera, coccoidea, pseudococcidae), like aphids and psyllids, are plant sap-sucking insects that have an obligate association with prokaryotic endosymbionts that are acquired through vertical, maternal transmission. we sequenced two fragments of the genome of tremblaya princeps, the endosymbiont of mealybugs, which is a member of the beta subdivision of the proteobacteria. each of the fragments (35 and 30 kb) contains a copy of 16s-23s-5s rrna genes. a total of 37 open reading fram ...	2002	12088995
50 million years of genomic stasis in endosymbiotic bacteria.	comparison of two fully sequenced genomes of buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. in contrast, the genomes of their closest free-living relatives, escherichia coli and salmonella spp., are more than 2000-fold more labile in content and g ...	2002	12089438
[identification of the horizontal gene transfer based on phylogenetic data].	we suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. the search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. numeric values are introduced to measure the discrepancy between the trees. this approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. this resulted in a list of the candidate genes ...	2003	12942641
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
facultative bacterial symbionts in aphids confer resistance to parasitic wasps.	symbiotic relationships between animals and microorganisms are common in nature, yet the factors controlling the abundance and distributions of symbionts are mostly unknown. aphids have an obligate association with the bacterium buchnera aphidicola (the primary symbiont) that has been shown to contribute directly to aphid fitness. in addition, aphids sometimes harbor other vertically transmitted bacteria (secondary symbionts), for which few benefits of infection have been previously documented. ...	2003	12563031
a matter of fitness.		2003	12648939
extraordinary proliferation of microorganisms in aposymbiotic pea aphids, acyrthosiphon pisum.	aposymbiotic pea aphids, which were deprived of their intracellular symbiotic bacterium, buchnera, exhibit growth retardation and no fecundity. high performance liquid chromatographic (hplc) analysis revealed that these aposymbiotic aphids, when reared on broad bean plants, accumulated a large amount of histamine. to assess the possibility of extraordinary proliferation of microorganisms other than buchnera, we enumerated eubacteria and fungi in aphids using the real-time quantitative pcr method ...	2003	12676551
why are the genomes of endosymbiotic bacteria so stable?	the comparative analysis of three strains of the endosymbiotic bacterium buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. the loss of genes involved in dna uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. gene loss, which was extensive during the initial steps of buchnera evolution, has continued in ...	2003	12683967
an appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction.	an exhaustive search for shortly spaced repeats in 74 bacterial chromosomes reveals that they are much more numerous than is usually acknowledged. these repeats were divided into five classes: close repeats (crs), tandem repeats (trs), simple sequence repeats (ssrs), spaced interspersed direct repeats, and "others." crs are widespread and constitute the most abundant class, particularly in coding sequences. the other classes are less frequent, but each individual element shows a higher potential ...	2003	12743022
low and homogeneous copy number of plasmid-borne symbiont genes affecting host nutrition in buchnera aphidicola of the aphid uroleucon ambrosiae.	the bacterial endosymbiont of aphids, buchnera aphidicola, often provides amino acids to its hosts. plasmid amplification of leucine (leuabcd) and tryptophan (trpeg) biosynthesis genes may be a mechanism by which some buchnera over-produce these nutrients. we used quantitative polymerase chain reaction to assess the leuabcd/trpeg copy variability within uroleucon ambrosiae, an aphid with a wide diet breadth and range. both leuabcd and trpeg abundances are: (i) similar for aphids across 15 popula ...	2003	12753227
reductive genome evolution in buchnera aphidicola.	we have sequenced the genome of the intracellular symbiont buchnera aphidicola from the aphid baizongia pistacea. this strain diverged 80-150 million years ago from the common ancestor of two previously sequenced buchnera strains. here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. as a consequence, the genome assembly unveiled intrapopulational variation, consisting of approximately 1,200 polymorphic sites. comparison of the 618-kb (kbp) g ...	2003	12522265
consequences of reductive evolution for gene expression in an obligate endosymbiont.	the smallest cellular genomes are found in obligate symbiotic and pathogenic bacteria living within eukaryotic hosts. in comparison with large genomes of free-living relatives, these reduced genomes are rearranged and have lost most regulatory elements. to test whether reduced bacterial genomes incur reduced regulatory capacities, we used full-genome microarrays to evaluate transcriptional response to environmental stress in buchnera aphidicola, the obligate endosymbiont of aphids. the 580 genes ...	2003	12791133
increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes.	mutualistic, maternally transmitted endosymbiotic microorganisms undergo severe population bottlenecks at each host generation, resulting in a reduction in effective population size (ne). previous studies of buchnera, the primary endosymbiont of aphids, and of several other species of endosymbiotic bacteria have shown that these species exhibit an increase in the rate of substitution of slightly deleterious mutations, among other predicted effects of increased drift due to small ne, such as redu ...	2003	12832648
the genome sequence of blochmannia floridanus: comparative analysis of reduced genomes.	bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. we present the complete genome sequence of blochmannia floridanus, the primary endosymbiont of carpenter ants. although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. remarkably, these bacteria lack all known ge ...	2003	12886019
host-based divergence in populations of the pea aphid: insights from nuclear markers and the prevalence of facultative symbionts.	in north america, the pea aphid acyrthosiphon pisum encompasses ecologically and genetically distinct host races that offer an ideal biological system for studies on sympatric speciation. in addition to its obligate symbiont buchnera, pea aphids harbour several facultative and phylogenetically distant symbionts. we explored the relationships between host races of a. pisum and their symbiotic microbiota to gain insights into the historical process of ecological specialization and symbiotic acquis ...	2003	12964998
a genomic perspective on nutrient provisioning by bacterial symbionts of insects.	many animals show intimate interactions with bacterial symbionts that provision hosts with limiting nutrients. the best studied such association is that between aphids and buchnera aphidicola, which produces essential amino acids that are rare in the phloem sap diet. genomic studies of buchnera have provided a new means for inferring metabolic capabilities of the symbionts and their likely contributions to hosts. despite evolutionary reduction of genome size, involving loss of most ancestral gen ...	2003	14527994
developmental origin and evolution of bacteriocytes in the aphid-buchnera symbiosis.	symbiotic relationships between bacteria and insect hosts are common. although the bacterial endosymbionts have been subjected to intense investigation, little is known of the host cells in which they reside, the bacteriocytes. we have studied the development and evolution of aphid bacteriocytes, the host cells that contain the endosymbiotic bacteria buchnera aphidicola. we show that bacteriocytes of acyrthosiphon pisum express several gene products (or their paralogues): distal-less, ultrabitho ...	2003	14551917
tracing the evolution of gene loss in obligate bacterial symbionts.	the gamma-proteobacterial symbionts of insects are a model group for comparative studies of genome reduction. the phylogenetic proximity of these reduced genomes to the larger genomes of well-studied free-living bacteria has enabled reconstructions of the process by which genes and dna are lost. three genome sequences are now available for buchnera aphidicola. analyses of buchnera genomes in comparison with those of related enteric bacteria suggest that extensive changes including large deletion ...	2003	14572545
automatic annotation of protein function based on family identification.	although genomes are being sequenced at an impressive rate, the information generated tells us little about protein function, which is slow to characterize by traditional methods. automatic protein function annotation based on computational methods has alleviated this imbalance. the most powerful current approach for inferring the function of new proteins is by studying the annotations of their homologues, since their common origin is assumed to be reflected in their structure and function. unfo ...	2003	14579359
diversity of bacteria associated with natural aphid populations.	the bacterial communities of aphids were investigated by terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis analysis of 16s rrna gene fragments generated by pcr with general eubacterial primers. by both methods, the gamma-proteobacterium buchnera was detected in laboratory cultures of six parthenogenetic lines of the pea aphid acyrthosiphon pisum and one line of the black bean aphid aphis fabae, and one or more of four previously described bacterial tax ...	2003	14660369
transmission of symbiotic bacteria buchnera to parthenogenetic embryos in the aphid acyrthosiphon pisum (hemiptera: aphidoidea).	all phloem-feeding aphids have an absolute requirement for their primary bacterial symbionts buchnera sp. the bacteria are transmitted vertically to either embryos in the viviparous morph or to eggs in the oviparous morph, with the implication that the symbiont population regularly passes through a genetic 'bottleneck', i.e. only a small proportion of the maternal symbiont population is transmitted to offspring. in this paper, we visualise this process in viviparous aphids using a specific immun ...	2003	18089009
chaos game representation of protein sequences based on the detailed hp model and their multifractal and correlation analyses.	similar to the chaos game representation (cgr) of dna sequences proposed by jeffrey (nucleic acid res. 18 (1990) 2163), a new cgr of protein sequences based on the detailed hp model is proposed. multifractal and correlation analyses of the measures based on the cgr of protein sequences from complete genomes are performed. the dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the cq curves to be meaningful. the cq curves of bacteria resemble a classical phase t ...	2004	14643648
mutational and selective pressures on codon and amino acid usage in buchnera, endosymbiotic bacteria of aphids.	we have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in escherichia coli, a close free-living relative. we sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the genomic changes following symbiosis. we identified clear strand asymmetries, distribu ...	2004	14672975
evolution of minimal-gene-sets in host-dependent bacteria.	several attempts have been made to identify the minimal set of genes that is required for life using computational approaches or studies of deletion mutants. these experiments resemble those already performed by nature; a few hundred million years ago an ancestor of escherichia coli was domesticated by aphids, which resulted in the elimination of 70-75% of the original bacterial genome. amazingly, the small genomes of these imprisoned bacteria are more stable than those of their free-living rela ...	2004	14700550
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
evolutionary relatedness between glycolytic enzymes most frequently occurring in genomes.	more than 100 sequenced genomes were searched for genes coding for the enzymes involved in glycolysis in an effort to find the most frequently occurring ones. triosephosphate isomerase (tim), glyceraldehyde-3-phosphate dehydrogenase (gapd), phosphoglycerate kinase (pgk) and enolase (enol) were found to be present in 90 investigated genomes all together. the final set consisted of 80 prokaryotic and 10 eukaryotic genomes. of the 80 prokaryotic genomes, 73 were from bacteria, 7 from archaea. two m ...	2004	15259764
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
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
molecular systematics of aphids (homoptera: aphididae): new insights from the long-wavelength opsin gene.	viviparous aphids (aphididae) constitute a monophyletic group within the homoptera with more than 4000 extant species worldwide but higher diversity in temperate regions. several aspects of their biology account for attention paid to this group of insects. their plant-sap-sucking way of feeding with many species transmitting viruses to crop plants has important implications on crop management strategies. cyclical parthenogenesis associated in many groups to host alternation and elaborate polyphe ...	2004	15022755
the relationship between palindrome avoidance and intragenic codon usage variations: a monte carlo study.	several studies have shown that codon usage within genes varies, as it seems dependent on both codon context and codon position within the gene. given that palindromes in addition often are avoided in genomes, this study aimed at finding out if intragenic variations in codon usage may be a way to control the amount and location of palindromes. a monte carlo algorithm was written which resampled the codons in genes while keeping the amino acid sequence of the translation product constant. on the ...	2004	15033465
use of the genomic signature in bacterial classification and identification.	in this study we investigated the correlation between dinucleotide relative abundance values (the genomic signature) obtained from bacterial whole-genome sequences and two parameters widely used for bacterial classification, 16s rdna sequence similarity and dna-dna hybridisation values. twenty-eight completely sequenced bacterial genomes were included in the study. the correlation between the genomic signature and dna-dna hybridisation values was high and taxa that showed less than 30% dna-dna b ...	2004	15046306
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
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
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
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
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
transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, buchnera.	aphids possess bacteriocytes, cells specifically differentiated to harbor obligatory mutualistic bacteria of the genus buchnera, which have lost many genes that are essential for common bacterial functions. to understand the host's role in maintaining the symbiotic relationship, bacteriocytes were isolated from the pea aphid, acyrthosiphon pisum, and the host transcriptome was investigated by using est analysis and real-time quantitative rt-pcr. a number of genes were highly expressed specifical ...	2005	15800043
comparative study of overlapping genes in bacteria, with special reference to rickettsia prowazekii and rickettsia conorii.	overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. in this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. the results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. the genomes of two closely related obligatory intracellular parasites - rickettsia prowazekii and ...	2005	15879256
endosymbiosis: past and present.		2005	15931237
gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria.	most endosymbiotic bacteria have extremely reduced genomes, accelerated evolutionary rates, and strong at base compositional bias thought to reflect reduced efficacy of selection and increased mutational pressure. here, we present a comparative study of evolutionary forces shaping five fully sequenced bacterial endosymbionts of insects. the results of this study were three-fold: (i) stronger conservation of high expression genes at not just nonsynonymous, but also synonymous, sites. (ii) variati ...	2005	15935576
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
rickettsia symbiont in the pea aphid acyrthosiphon pisum: novel cellular tropism, effect on host fitness, and interaction with the essential symbiont buchnera.	in natural populations of the pea aphid acyrthosiphon pisum, a facultative bacterial symbiont of the genus rickettsia has been detected at considerable infection frequencies worldwide. we investigated the effects of the rickettsia symbiont on the host aphid and also on the coexisting essential symbiont buchnera. in situ hybridization revealed that the rickettsia symbiont was specifically localized in two types of host cells specialized for endosymbiosis: secondary mycetocytes and sheath cells. e ...	2005	16000822
the roles of positive and negative selection in the molecular evolution of insect endosymbionts.	the evolutionary rate acceleration observed in most endosymbiotic bacteria may be explained by higher mutation rates, changes in selective pressure, and increased fixation of deleterious mutations by genetic drift. here, we explore the forces influencing molecular evolution in blochmannia, an obligate endosymbiont of camponotus and related ant genera. our goals were to compare rates of sequence evolution in blochmannia with related bacteria, to explore variation in the strength and efficacy of n ...	2005	16039807
genome sequence of blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects.	the distinct lifestyle of obligately intracellular bacteria can alter fundamental forces that drive and constrain genome change. in this study, sequencing the 792-kb genome of blochmannia pennsylvanicus, an obligate endosymbiont of camponotus pennsylvanicus, enabled us to trace evolutionary changes that occurred in the context of a bacterial-ant association. comparison to the genome of blochmannia floridanus reveals differential loss of genes involved in cofactor biosynthesis, the composition an ...	2005	16077009
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
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
nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-proteobacteria).	standard methods of phylogenetic reconstruction are based on models that assume homogeneity of nucleotide composition among taxa. however, this assumption is often violated in biological data sets. in this study, we examine possible effects of nucleotide heterogeneity among lineages on the phylogenetic reconstruction of a bacterial group that spans a wide range of genomic nucleotide contents: obligately endosymbiotic bacteria and free-living or commensal species in the gamma-proteobacteria. we f ...	2005	15525700
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
buchnerabase: a post-genomic resource for buchnera sp. aps.	summary: buchnerabase is a bioinformatic research tool for the genome of the symbiotic bacterium buchnera sp. aps that includes an improved genome annotation, comparative information about related insect symbiont genomes and a complete mapping of metabolic reactions to an escherichia coli in silico model. the database is designed to accommodate genome-wide post-genomic datasets that are becoming available for this organism. availability: buchnerabase is available at http://www.buchnera.org/.	2006	16397006
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
phloem-sap feeding by animals: problems and solutions.	the incidence of phloem sap feeding by animals appears paradoxical. although phloem sap is nutrient-rich compared with many other plant products and generally lacking in toxins and feeding deterrents, it is consumed as the dominant or sole diet by a very restricted range of animals, exclusively insects of the order hemiptera. these insects display two sets of adaptations. first, linked to the high ratio of non-essential:essential amino acids in phloem sap, these insects contain symbiotic micro-o ...	2006	16449374
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
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
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
functional genomics of buchnera and the ecology of aphid hosts.	in many animal groups, mutualistic bacterial symbionts play a central role in host ecology, by provisioning rare nutrients and thus enabling specialization on restricted diets. among such symbionts, genomic studies are most advanced for buchnera, the obligate symbiont of aphids, which feed on phloem sap. the contents of the highly reduced buchnera genomes have verified its role in aphid nutrition. comparisons of buchnera gene sets indicate ongoing, irreversible gene losses that are expected to a ...	2006	16626452
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
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
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
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
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
genetics. the bacterial world gets smaller.		2006	17038609
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
the reach of the genome signature in prokaryotes.	with the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. one of these studies suggested good congruence between genome synteny, shared gene content, 16s ribosomal dna identity, codon usage and the genome signature in prokaryotes. here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced pr ...	2006	17040564
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
selection acts on dna secondary structures to decrease transcriptional mutagenesis.	single-stranded dna is more subject to mutation than double stranded. during transcription, dna is transiently single stranded and therefore subject to higher mutagenesis. however, if local intra-strand secondary structures are formed, some bases will be paired and therefore less sensitive to mutation than unpaired bases. using complete genome sequences of escherichia coli, we show that local intra-strand secondary structures can, as a consequence, be used to define an index of transcription-dri ...	2006	17083275
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
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
role of host nutrition in symbiont regulation: impact of dietary nitrogen on proliferation of obligate and facultative bacterial endosymbionts of the pea aphid acyrthosiphon pisum.	the impact of host nutrition on symbiont regulation in the pea aphid acyrthosiphon pisum was investigated. the population density of the obligate symbiont buchnera aphidicola positively correlated with dietary nitrogen levels. in contrast, the population density of the facultative symbiont serratia symbiotica increased in aphids reared on low-nitrogen diets, indicating distinct regulatory mechanisms in the same insect host.	2007	17158610
evolutionary relationships of "candidatus riesia spp.," endosymbiotic enterobacteriaceae living within hematophagous primate lice.	the primary endosymbiotic bacteria from three species of parasitic primate lice were characterized molecularly. we have confirmed the characterization of the primary endosymbiont (p-endosymbiont) of the human head/body louse pediculus humanus and provide new characterizations of the p-endosymbionts from pediculus schaeffi from chimpanzees and pthirus pubis, the pubic louse of humans. the endosymbionts show an average percent sequence divergence of 11 to 15% from the most closely related known ba ...	2007	17220259
selective elimination of aphid endosymbionts: effects of antibiotic dose and host genotype, and fitness consequences.	multiple endosymbionts commonly coexist in the same host insects. in order to gain an understanding of the biological roles of the individual symbionts in such complex systems, experimental techniques for enabling the selective removal of a specific symbiont from the host are of great importance. by using the pea aphid-buchnera-serratia endosymbiotic system as a model, the efficacy, generality, and fitness consequences of selective elimination techniques at various antibiotic doses and under a v ...	2007	17313660
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
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
optimization and clinical validation of a pathogen detection microarray.	dna microarrays used as 'genomic sensors' have great potential in clinical diagnostics. biases inherent in random pcr-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. novel features of this platform include the development of a robust ...	2007	17531104
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
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
antibiotics, primary symbionts and wing polyphenism in three aphid species.	the possible role of the primary buchnera symbionts in wing polyphenism is examined in three aphid species. presumptive winged aphids were fed on antibiotic-treated beans to destroy these symbionts. as previously reported, this leads to inhibited growth and low/zero fecundity. when such treatment is applied to the short-day-induced gynoparae (the winged autumn migrant) of the black bean aphid, aphis fabae, it also causes many insects to develop as wingless or winged/wingless intermediate adult f ...	2007	17628287
temporal fragmentation of speciation in bacteria.	because bacterial recombination involves the occasional transfer of small dna fragments between strains, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci. therefore, genetic isolation may be established at different times for different chromosomal regions during speciation as recombination at niche-specific genes is curtailed. to test this model, we separated sequence divergence into rate and time components, revealing that different reg ...	2007	17717188
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
how do endosymbionts become organelles? understanding early events in plastid evolution.	what factors drove the transformation of the cyanobacterial progenitor of plastids (e.g. chloroplasts) from endosymbiont to bona fide organelle? this question lies at the heart of organelle genesis because, whereas intracellular endosymbionts are widespread in both unicellular and multicellular eukaryotes (e.g. rhizobial bacteria, chlorella cells in ciliates, buchnera in aphids), only two canonical eukaryotic organelles of endosymbiotic origin are recognized, the plastids of algae and plants and ...	2007	18027391
when bacteria lose a single dna base, aphids suffer.		2007	20076671
muller's ratchet in symbiont populations.	muller's ratchet, the inevitable accumulation of deleterious mutations in asexual populations, has been proposed as a major factor in genome degradation of obligate symbiont organisms. essentially, if left unchecked the ratchet will with certainty cause extinction due to the ever increasing mutational load. this paper examines the evolutionary fate of insect symbionts, using mathematical modelling to simulate the accumulation of deleterious mutations. we investigate the effects of a hierarchical ...	2007	16924405
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
plasmids derived from gifsy-1/gifsy-2, lambdoid prophages contributing to the virulence of salmonella enterica serovar typhimurium: implications for the evolution of replication initiation proteins of lambdoid phages and enterobacteria.	gifsy-1 and gifsy-2 are lambdoid prophages which contribute to the virulence of salmonella enterica serovar typhimurium. the nucleotide sequence of the replication region of both prophages is identical, and similar in organization to the replication region of bacteriophage lambda. to investigate the replication of the gifsy phages and the relationship between gifsy and host chromosome replication, a plasmid which contained all the genes and regulatory sequences required for autonomous replicatio ...	2007	17526845
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
impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage.	the effective number of codons (nc) used in a gene is one of the most commonly used measures of synonymous codon usage bias, owing much of its popularity to the fact that it is species independent and that simulation studies have shown that it is less dependent of gene length than other measures. in this paper i provide a clear and practically meaningful definition of bias discrepancy (bd; when the degree of codon bias varies within a degeneracy class). moreover i evaluate the impact of bd and a ...	2008	18248919