Publications

coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam calyptogena magnifica.	the hydrothermal vent clam calyptogena magnifica (bivalvia: vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. this symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. if symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if ...	2003	12676683
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
comparing bacterial genomes through conservation profiles.	we constructed two-dimensional representations of profiles of gene conservation across different genomes using the genome of escherichia coli as a model. these profiles permit both the visualization at the genome level of different traits in the organism studied and, at the same time, reveal features related to the genomes analyzed (such as defective genomes or genomes that lack a particular system). conserved genes are not uniformly distributed along the e. coli genome but tend to cluster toget ...	2003	12695324
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
crystal structure of trna(m1g37)methyltransferase: insights into trna recognition.	trna(m(1)g37)methyltransferase (trmd) catalyzes the transfer of a methyl group from s-adenosyl-l- methionine (adomet) to g(37) within a subset of bacterial trna species, which have a g residue at the 36th position. the modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. here we report four crystal structures of trmd from haemophilus influenzae, as binary complexes with either adomet or s-adenosyl-l-homocy ...	2003	12773376
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
developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through hisf.	hish-hisf is a multidomain globular protein complex; hish is a class i glutamine amidotransferase that hydrolyzes glutamine to form ammonia, and hisf is a (beta/alpha)8 barrel cyclase that completes the ring formation of imidizole glycerol phosphate synthase. together, hish and hisf form a glutamine amidotransferase that carries out the fifth step of the histidine biosynthetic pathway. recently, it has been suggested that the (beta/alpha)8 barrel participates in a novel function: to channel ammo ...	2003	12799468
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
ancient origin of the tryptophan operon and the dynamics of evolutionary change.	the seven conserved enzymatic domains required for tryptophan (trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. a comparative bioinformatics evaluation of the conservation and organization of the genes of trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and oper ...	2003	12966138
from gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria.	the rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. however, extensive lateral gene transfer (lgt) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. the group for which cases of lgt are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-proteobacteria, an ...	2003	12975657
gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.	lineage-specific gene loss, to a large extent, accounts for the differences in gene repertoires between genomes, particularly among eukaryotes. we derived a parsimonious scenario of gene losses for eukaryotic orthologous groups (kogs) from seven complete eukaryotic genomes. the scenario involves substantial gene loss in fungi, nematodes, and insects. based on this evolutionary scenario and estimates of the divergence times between major eukaryotic phyla, we introduce a numerical measure, the pro ...	2003	14525925
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
functionality of system components: conservation of protein function in protein feature space.	many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties. we show here that such protein features are more conserved among orthologs than paralogs, indicating they are crucial for protein function and thus subject to selective pressure. this means that a function prediction method based on sequence-derived features may be able to discriminate between protei ...	2003	14559779
the genome of nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism.	the hyperthermophile nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon ignicoccus. ribosomal protein and rrna-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom nanoarchaeota. the n. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. it is the smallest microbial genome seque ...	2003	14566062
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
extensive repetitive dna facilitates prokaryotic genome plasticity.	prokaryotic genomes are substantially diverse, even when from closely related species, with the resulting phenotypic diversity representing a repertoire of adaptations to specific constraints. within the microbial population, genome content may not be fixed, as changing selective forces favor particular phenotypes; however, organisms well adapted to particular niches may have evolved mechanisms to facilitate such plasticity. the highly diverse helicobacter pylori is a model for studying genome p ...	2003	14593200
identification and characterization of phytoplasmal genes, employing a novel method of isolating phytoplasmal genomic dna.	phytoplasmas are unculturable, insect-transmissible plant pathogens belonging to the class mollicutes. to be transmitted, the phytoplasmas replicate in the insect body and are delivered to the insect's salivary glands, from where they are injected into the recipient plant. because phytoplasmas cannot be cultured, any attempt to recover phytoplasmal dna from infected plants or insects has resulted in preparations with a large background of host dna. thus, studies of the phytoplasmal genome have b ...	2003	14594823
enzyme-specific profiles for genome annotation: priam.	the advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. here we describe priam, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the enzyme database. priam relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each enzyme entry. automatically generated logical rules define which of these profile ...	2003	14602924
a key role for the mrna leader structure in translational control of ribosomal protein s1 synthesis in gamma-proteobacteria.	the translation initiation region (tir) of the escherichia coli rpsa mrna coding for ribosomal protein s1 is characterized by a remarkable efficiency in driving protein synthesis despite the absence of the canonical shine-dalgarno element, and by a strong and specific autogenous repression in the presence of free s1 in trans. the efficient and autoregulated e.coli rpsa tir comprises not less than 90 nt upstream of the translation start and can be unambiguously folded into three irregular hairpin ...	2003	14627832
ccpa-dependent carbon catabolite repression in bacteria.	carbon catabolite repression (ccr) by transcriptional regulators follows different mechanisms in gram-positive and gram-negative bacteria. in gram-positive bacteria, ccpa-dependent ccr is mediated by phosphorylation of the phosphoenolpyruvate:sugar phosphotransferase system intermediate hpr at a serine residue at the expense of atp. the reaction is catalyzed by hpr kinase, which is activated by glycolytic intermediates. in this review, the distribution of ccpa-dependent ccr among bacteria is inv ...	2003	14665673
growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis p) in escherichia coli.	the intracellular concentration of the escherichia coli factor for inversion stimulation (fis), a global regulator of transcription and a facilitator of certain site-specific dna recombination events, varies substantially in response to changes in the nutritional environment and growth phase. under conditions of nutritional upshift, fis is transiently expressed at very high levels, whereas under induced starvation conditions, fis is repressed by stringent control. we show that both of these regu ...	2004	14679232
a conservative test of genetic drift in the endosymbiotic bacterium buchnera: slightly deleterious mutations in the chaperonin groel.	the obligate endosymbiotic bacterium buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. because buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. recent studies of intraspecific variation in buchnera reveal patterns consistent with this hypo ...	2003	14704156
changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont buchnera in an aphid.	almost all aphids harbour an endosymbiotic bacterium, buchnera aphidicola, in bacteriocytes. buchnera synthesizes essential nutrients and supports growth and reproduction of the host. over the long history of endosymbiosis, many essential genes have been lost from the buchnera genome, resulting in drastic genome reduction and the inability to live outside the host cells. in turn, when deprived of buchnera, the host aphid suffers retarded growth and sterility. buchnera and the host aphid are ofte ...	2003	14728775
cassette-like variation of restriction enzyme genes in escherichia coli c and relatives.	a surprising result of comparative bacterial genomics has been the large amount of dna found to be present in one strain but not in another of the same species. we examine in detail one location where gene content varies extensively, the restriction cluster in escherichia coli. this region is designated the immigration control region (icr) for the density and variability of restriction functions found there. to better define the boundaries of this variable locus, we determined the sequence of th ...	2004	14744977
host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia.	bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. candidatus blochmannia gen. nov. (blochmannia) is an obligate bacterial associate of camponotus and related ant genera (hymenoptera: formicidae). the occurrence of blochmannia in all camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, sta ...	2004	14965905
prediction of rna-binding proteins from primary sequence by a support vector machine approach.	elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. computational methods have been developed for the prediction of protein-protein interactions. but insufficient attention has been paid to the prediction of protein-rna interactions, which play central roles in regulating gene expression and certain rna-mediated enzymatic processes. this work explored the use of a machine learning method, support vector machines (svm) ...	2004	14970381
evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of paederus fuscipes beetles.	pederin belongs to a group of antitumor compounds found in terrestrial beetles and marine sponges. it is used by apparently all members of the rove beetle genera paederus and paederidus as a chemical defense against predators. however, a recent analysis of the putative pederin biosynthesis (ped) gene cluster strongly suggests that pederin is produced by bacterial symbionts. we have sequenced an extended region of the symbiont genome to gain further insight into the biology of this as-yet-uncultu ...	2004	14973122
a phylogenomic study of endosymbiotic bacteria.	endosymbiotic bacteria of aphids, buchnera aphidicola, and tsetse flies, wigglesworthia glossinidia, are descendents of free-living gamma-proteobacteria. the acceleration of sequence evolution in the endosymbiont genomes is here estimated from a phylogenomic analysis of the gamma-proteobacteria. the tree topologies associated with the most highly conserved genes suggest that the endosymbionts form a sister group with escherichia coli, salmonella sp., and yersinia pestis. our results indicate tha ...	2004	15014155
comparative genomics of gene-family size in closely related bacteria.	the wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear.	2004	15059260
transgenic expression of reca of the spirochetes borrelia burgdorferi and borrelia hermsii in escherichia coli revealed differences in dna repair and recombination phenotypes.	after unsuccessful attempts to recover a viable reca-deficient mutant of the lyme borreliosis agent borrelia burgdorferi, we characterized the functional activities of reca of b. burgdorferi, as well as reca of the relapsing fever spirochete borrelia hermsii and the free-living spirochete leptospira biflexa, in a reca mutant of escherichia coli. as a control, e. coli reca was expressed from the same plasmid vector. dna damage repair activity was assessed after exposure of the transgenic cells to ...	2004	15060027
properties of bacillus subtilis sigma a factors with region 1.1 and the conserved arg-103 at the n terminus of region 1.2 deleted.	sigma factors in the sigma(70) family can be classified into the primary and alternative sigma factors according to their physiological functions and amino acid sequence similarities. the primary sigma factors are composed of four conserved regions, with the conserved region 1 being divided into two subregions. region 1.1, which is absent from the alternative sigma factor, is poor in conservation; however, region 1.2 is well conserved. we investigated the importance of these two subregions to th ...	2004	15060039
analysis of an engineered salmonella flagellar fusion protein, flir-flhb.	salmonella flir and flhb are membrane proteins necessary for flagellar export. in clostridium a flir-flhb fusion gene exists. we constructed a similar salmonella fusion gene which is able to complement flir, flhb, and flir flhb null strains. western blotting revealed that the flir-flhb fusion protein retains the flhb protein's cleavage properties. we conclude that the flir and flhb proteins are physically associated in the wild-type salmonella basal body, probably in a 1:1 ratio.	2004	15060055
fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy.	a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ...	2004	15060178
assessment of 35mer amino-modified oligonucleotide based microarray with bacterial samples.	parallel quantification of a large number of messenger rna transcripts, using microarray technology, promises to provide unsuspected information about many cellular processes. although experimental protocols on microarray applications are available, only limited methodological information on glass-slide manufacturing and signal interpretation has been published. the aim of this paper is to provide new insights into the practical aspects of the construction and hybridization of oligonucleotide-ba ...	2004	15063061
microorganisms resistant to free-living amoebae.	free-living amoebae feed on bacteria, fungi, and algae. however, some microorganisms have evolved to become resistant to these protists. these amoeba-resistant microorganisms include established pathogens, such as cryptococcus neoformans, legionella spp., chlamydophila pneumoniae, mycobacterium avium, listeria monocytogenes, pseudomonas aeruginosa, and francisella tularensis, and emerging pathogens, such as bosea spp., simkania negevensis, parachlamydia acanthamoebae, and legionella-like amoebal ...	2004	15084508
evolution of the leucine gene cluster in buchnera aphidicola: insights from chromosomal versions of the cluster.	in buchnera aphidicola strains associated with the aphid subfamilies thelaxinae, lachninae, pterocommatinae, and aphidinae, the four leucine genes (leua, -b, -c, and -d) are located on a plasmid. however, these genes are located on the main chromosome in b. aphidicola strains associated with the subfamilies pemphiginae and chaitophorinae. the sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in b. aphidicola strains a ...	2004	15090505
prolinks: a database of protein functional linkages derived from coevolution.	the advent of whole-genome sequencing has led to methods that infer protein function and linkages. we have combined four such algorithms (phylogenetic profile, rosetta stone, gene neighbor and gene cluster) in a single database--prolinks--that spans 83 organisms and includes 10 million high-confidence links. the proteome navigator tool allows users to browse predicted linkage networks interactively, providing accompanying annotation from public databases. the prolinks database and the proteome n ...	2004	15128449
a novel alpha-proteobacterium resides in the mitochondria of ovarian cells of the tick ixodes ricinus.	an intracellular bacterium from ixodes ricinus ticks collected in italy was characterized by electron microscopy (em), pcr sequencing of the 16s rrna gene, molecular phylogenetic analysis, and in situ hybridization (ish). this bacterium was shown by em to be present in the cytoplasm, as well as in the mitochondria of ovarian cells. when universal 16s rrna bacterial primers were used, pcr amplification of ovarian dna followed by cloning and sequencing resulted in the same sequence being found in ...	2004	15128508
predicting transmembrane beta-barrels in proteomes.	very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. one reason is that only very few high-resolution structures for transmembrane beta-barrel (tmb) proteins have been determined thus far. here we introduced the design, statistics and results of a novel profile-based hidden markov model for the prediction and discrimination of tmbs. the method carefully attempts to avoid over-fitting the sparse experimental data. while our model training and sc ...	2004	15141026
sequence motifs that distinguish atp(ctp):trna nucleotidyl transferases from eubacterial poly(a) polymerases.	atp(ctp):trna nucleotidyl transferases, trna maturing enzymes found in all organisms, and eubacterial poly(a) polymerases, enzymes involved in mrna degradation, are so similar that until now their biochemical functions could not be distinguished by their amino acid sequence. blast searches and analysis with the program "sequence space" for the prediction of functional residues revealed sequence motifs which define these two protein families. one of the poly(a) polymerase defining motifs specifie ...	2004	15146073
global analysis of predicted proteomes: functional adaptation of physical properties.	the physical characteristics of proteins are fundamentally important in organismal function. we used the complete predicted proteomes of >100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. theoretical 2d gels were constructed with axes of protein mass and charge (pi) and converted to density estimates comparable across all types and sizes of proteome. we asked whether we could detect general patterns of proteome conservation and va ...	2004	15150418
bacterial genomes as new gene homes: the genealogy of orfans in e. coli.	differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. however, most bacteria contain large numbers of orfans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. the uniqueness of orfans within a genome has precluded the use of a comparative approach to examine their function and evolution. however, by identifying sequences unique to monophyletic g ...	2004	15173110
evolutionary relationships of primary prokaryotic endosymbionts of whiteflies and their hosts.	whiteflies (hemiptera: sternorrhyncha: aleyrodidae) are plant sap-sucking insects that harbor prokaryotic primary endosymbionts (p-endosymbionts) within specialized cells located in their body cavity. four-kilobase dna fragments containing 16s-23s ribosomal dna (rdna) were amplified from the p-endosymbiont of 24 whiteflies from 22 different species of 2 whitefly subfamilies. in addition, 3-kb dna fragments containing mitochondrial cytb, nd1, and large-subunit rdna (lrdna) were amplified from 17 ...	2004	15184137
inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.	the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ...	2004	15214963
replication of the endosymbiotic bacterium blochmannia floridanus is correlated with the developmental and reproductive stages of its ant host.	the dynamics of replication of the intracellular endosymbiotic bacterium blochmannia floridanus was determined during the larval development of its host ant camponotus floridanus by real-time quantitative pcr. the bacteria were found to proliferate during pupation and immediately after the eclosion of the imagines (adult ants). in older workers the number of bacteria present in the midgut bacteriocytes decreased significantly. in contrast, the bacterial population in the ovaries was dependent on ...	2004	15240288
proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison.	we propose a new method for classifying and identifying transmembrane (tm) protein functions in proteome-scale by applying a single-linkage clustering method based on tm topology similarity, which is calculated simply from comparing the lengths of loop regions. in this study, we focused on 87 prokaryotic tm proteomes consisting of 31 proteobacteria, 22 gram-positive bacteria, 19 other bacteria, and 15 archaea. prior to performing the clustering, we first categorized individual tm protein sequenc ...	2004	15273311
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
determination of the core of a minimal bacterial gene set.	the availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. the availabl ...	2004	15353568
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
abstracts of the fourth international symposium on molecular insect science. may 28-june 2, 2002. tucson, arizona, usa.		2002	15455051
crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis.	gamma-glutamylcysteine synthetase (gammagcs), a rate-limiting enzyme in glutathione biosynthesis, plays a central role in glutathione homeostasis and is a target for development of potential therapeutic agents against parasites and cancer. we have determined the crystal structures of escherichia coli gammagcs unliganded and complexed with a sulfoximine-based transition-state analog inhibitor at resolutions of 2.5 and 2.1 a, respectively. in the crystal structure of the complex, the bound inhibit ...	2004	15477603
analysis of the cytoplasmic domains of salmonella flha and interactions with components of the flagellar export machinery.	most flagellar proteins are exported via a type iii export apparatus which, in part, consists of the membrane proteins flha, flhb, flio, flip, fliq, and flir and is housed within the membrane-supramembrane ring formed by flif subunits. salmonella flha is a 692-residue integral membrane protein with eight predicted transmembrane spans. its function is not understood, but it is necessary for flagellar export. we have created mutants in which potentially important sequences were deleted. flha lacki ...	2004	15516571
a genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land.	the timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. however, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. we assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species ...	2004	15535883
structural similarity of ybed protein from escherichia coli to allosteric regulatory domains.	lipoic acid is an essential prosthetic group in several metabolic pathways. the biosynthetic pathway of protein lipoylation in escherichia coli involves gene products of the lip operon. ybed is a conserved bacterial protein located in the daca-lipb intergenic region. here, we report the nuclear magnetic resonance structure of ybed from e. coli. the structure includes a beta alpha beta beta alpha beta fold with two alpha-helices on one side of a four-strand antiparallel beta-sheet. the beta 2-bet ...	2004	15547281
evolutionary relationships of fusobacterium nucleatum based on phylogenetic analysis and comparative genomics.	the phylogenetic position and evolutionary relationships of fusobacteria remain uncertain. especially intriguing is their relatedness to low g+c gram positive bacteria (firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. taking advantage of the recent completion of the fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of fusobacterium genes by phylogenetic analysis and comparative genomics tools.	2004	15566569
the rpoh-mediated stress response in neisseria gonorrhoeae is regulated at the level of activity.	the general stress response in neisseria gonorrhoeae was investigated. transcriptional analyses of the genes encoding the molecular chaperones dnak, dnaj, and grpe suggested that they are transcribed from sigma32 (rpoh)-dependent promoters upon exposure to stress. this was confirmed by mutational analysis of the sigma32 promoter of dnak. the gene encoding the gonococcal rpoh sigma factor appears to be essential, as we could not isolate viable mutants. deletion of an unusually long rpoh leader se ...	2004	15576794
new insights into type ii nad(p)h:quinone oxidoreductases.	type ii nad(p)h:quinone oxidoreductases (ndh-2) catalyze the two-electron transfer from nad(p)h to quinones, without any energy-transducing site. ndh-2 accomplish the turnover of nad(p)h, regenerating the nad(p)(+) pool, and may contribute to the generation of a membrane potential through complexes iii and iv. these enzymes are usually constituted by a nontransmembrane polypeptide chain of approximately 50 kda, containing a flavin moiety. there are a few compounds that can prevent their activity ...	2004	15590775
metagenomics: application of genomics to uncultured microorganisms.	metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of dna from an assemblage of microorganisms. the development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. this evidence was derived from analyses of 16s rrna gene sequences amplified directly from the environment, an approach that avo ...	2004	15590779
metabolic interdependence of obligate intracellular bacteria and their insect hosts.	mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. however, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell. this review attempts to provide insights into the complex physiological interactions and the evolution of m ...	2004	15590782
mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.	the influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. here, we explore the impact of mutation and selection on the dynamics of synonymous changes in buchnera aphidicola, the at-rich bacterial endosymbiont of aphids. specifically, we evaluated three ...	2004	15599516
tractor_db: a database of regulatory networks in gamma-proteobacterial genomes.	experimental data on the escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (tfs), tfs' binding sites and operons) within its genome. as more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcrip ...	2005	15608293
tractor_db: a database of regulatory networks in gamma-proteobacterial genomes.	experimental data on the escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (tfs), tfs' binding sites and operons) within its genome. as more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcrip ...	2005	15608293
a nomenclature for all signal recognition particle rnas.	the signal recognition particle (srp) is a cytosolic ribonucleoprotein complex that guides secretory proteins to biological membranes in all organisms. the srp rna is at the center of the structure and function of the srp. the comparison of the growing number of srp rna sequences provides a rich source for gaining valuable insight into the composition, assembly, and phylogeny of the srp. in order to assist in the continuation of these studies, we propose an srp rna nomenclature applicable to the ...	2005	15611297
differences in codon bias cannot explain differences in translational power among microbes.	translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. one factor known to affect translational power is biased use of synonymous codons. the correlation within an organism between expression level and degree of codon bias among genes of escherichia coli and other bact ...	2005	15636642
accelerated evolution associated with genome reduction in a free-living prokaryote.	three complete genomes of prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in g+c content. as all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in prochlorococcus is the first documen ...	2005	15693943
pseudomonas aeruginosa mutl protein functions in escherichia coli.	escherichia coli muts, mutl and muth proteins act sequentially in the mmrs (mismatch repair system). muth directs the repair system to the newly synthesized strand due to its transient lack of dam (dna-adenine methylase) methylation. although pseudomonas aeruginosa does not have the corresponding e. coli muth and dam homologues, and consequently the mmrs seems to work differently, we show that the mutl gene from p. aeruginosa is capable of complementing a mutl-deficient strain of e. coli. mutl f ...	2005	15709980
comparative analysis of two genomic regions among four strains of buchnera aphidicola, primary endosymbiont of aphids.	preliminary analysis of two selected genomic regions of buchnera aphidicola bcc, the primary endosymbiont of the cedar aphid cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three b. aphidicola genomes previously sequenced, that are associated with different aphid species. both regions exhibit a significant reduction in length and gene number in b. aphidicola bcc, as it could be expected since it possess the smallest bacte ...	2004	15716086
variation in the strength of selected codon usage bias among bacteria.	among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. however, in other species selection appears to have been ineffective. here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. the approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. the ...	2005	15728743
bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion.	like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ...	2005	15757514
genome rearrangement distances and gene order phylogeny in gamma-proteobacteria.	genome rearrangements have been studied in 30 gamma-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. this set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. genome rearrangement distances were estimated based on either the number of breakpoints or the minimal number of inversions separating two genomes. ...	2005	15772379
the wolbachia genome of brugia malayi: endosymbiont evolution within a human pathogenic nematode.	complete genome dna sequence and analysis is presented for wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode brugia malayi. although, quantitatively, the genome is even more degraded than those of closely related rickettsia species, wolbachia has retained more intact metabolic pathways. the ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be wolbachia's principal co ...	2005	15780005
evolutionary origins of genomic repertoires in bacteria.	explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. in eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (lgt) can also contribute substantially to genome contents. to determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the gamma-proteobacteria. we show that, although the ...	2005	15799709
systematic association of genes to phenotypes by genome and literature mining.	one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ...	2005	15799710
deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.	when organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. indeed, even when the true ...	2005	15819979
solution structure of the carbon storage regulator protein csra from escherichia coli.	the carbon storage regulator a (csra) is a protein responsible for the repression of a variety of stationary-phase genes in bacteria. in this work, we describe the nuclear magnetic resonance (nmr)-based structure of the csra dimer and its rna-binding properties. csra is a dimer of two identical subunits, each composed of five strands, a small alpha-helix and a flexible c terminus. nmr titration experiments suggest that the beta1-beta2 and beta3-beta4 loops and the c-terminal helix are important ...	2005	15866937
global divergence of microbial genome sequences mediated by propagating fronts.	we model the competition between homologous recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. depending on the specifics of homologous recombination, we find that global sequence divergence can be mediated by fronts propagating along the genome, whose characteristic signature on genome structure is elucidated, and apparently observed in closely related bacillus strains. front propagation provides an em ...	2005	15878987
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
identification of genomic features using microsyntenies of domains: domain teams.	the detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). our approach adopts the technique of temporarily forgetting genes and working directly with p ...	2005	15899966
a multidomain fusion protein in listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis.	glutathione is the predominant low-molecular-weight peptide thiol present in living organisms and plays a key role in protecting cells against oxygen toxicity. until now, glutathione synthesis was thought to occur solely through the consecutive action of two physically separate enzymes, gamma-glutamylcysteine ligase and glutathione synthetase. in this report we demonstrate that listeria monocytogenes contains a novel multidomain protein (termed gshf) that carries out complete synthesis of glutat ...	2005	15901709
prediction of functional modules based on comparative genome analysis and gene ontology application.	we present a computational method for the prediction of functional modules encoded in microbial genomes. in this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. we first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and gene ontology ass ...	2005	15901854
evolutionary relationships of three new species of enterobacteriaceae living as symbionts of aphids and other insects.	ecological studies on three bacterial lineages symbiotic in aphids have shown that they impose a variety of effects on their hosts, including resistance to parasitoids and tolerance to heat stress. phylogenetic analyses of partial sequences of gyrb and reca are consistent with previous analyses limited to 16s rrna gene sequences and yield improved confidence of the evolutionary relationships of these symbionts. all three symbionts are in the enterobacteriaceae. one of the symbionts, here given t ...	2005	15933033
regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont buchnera aphidicola.	buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. using full-genome microarrays for b. aphidicola of the host schizaphis graminum, we examined transcriptome respon ...	2005	15937185
protein length in eukaryotic and prokaryotic proteomes.	we analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. comparing eukaryotes and prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. the magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended m ...	2005	15951512
the genome sequence of rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite.	we sequenced the genome of rickettsia felis, a flea-associated obligate intracellular alpha-proteobacterium causing spotted fever in humans. besides a circular chromosome of 1,485,148 bp, r. felis exhibits the first putative conjugative plasmid identified among obligate intracellular bacteria. this plasmid is found in a short (39,263 bp) and a long (62,829 bp) form. r. felis contrasts with previously sequenced rickettsia in terms of many other features, including a number of transposases, severa ...	2005	15984913
extrachromosomal dna of the symbiont sodalis glossinidius.	the extrachromosomal dna of sodalis glossinidius from two tsetse fly species was sequenced and contained four circular elements: three plasmids, psg1 (82 kb), psg2 (27 kb), and psg4 (11 kb), and a bacteriophage-like psg3 (19 kb) element. the information suggests s. glossinidius is evolving towards an obligate association with tsetse flies.	2005	15995217
systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops.	public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. the available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops.	2005	16011797
mosaic nature of the wolbachia surface protein.	lateral gene transfer and recombination play important roles in the evolution of many parasitic bacteria. here we investigate intragenic recombination in wolbachia bacteria, considered among the most abundant intracellular bacteria on earth. we conduct a detailed analysis of the patterns of variation and recombination within the wolbachia surface protein, utilizing an extensive set of published and new sequences from five main supergroups of wolbachia. analysis of nucleotide and amino acid seque ...	2005	16030235
the bacteriophage p1 hot gene product can substitute for the escherichia coli dna polymerase iii {theta} subunit.	the theta subunit (hole gene product) of escherichia coli dna polymerase (pol) iii holoenzyme is a tightly bound component of the polymerase core. within the core (alpha-epsilon-theta), the alpha and epsilon subunits carry the dna polymerase and 3' proofreading functions, respectively, while the precise function of theta is unclear. hole homologs are present in genomes of other enterobacteriae, suggestive of a conserved function. putative homologs have also been found in the genomes of bacteriop ...	2005	16077097
phylogenetic analysis of pasteuria penetrans by use of multiple genetic loci.	pasteuria penetrans is a gram-positive, endospore-forming eubacterium that apparently is a member of the bacillus-clostridium clade. it is an obligate parasite of root knot nematodes (meloidogyne spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. consequently, p. penetrans has long been recognized as a potential biocontrol agent for root knot nematode ...	2005	16077116
resistance is costly: trade-offs between immunity, fecundity and survival in the pea aphid.	parasitoids are among the most important natural enemies of insects in many environments. acyrthosiphon pisum, the pea aphid, is a common pest of the leguminous crops in temperate regions. pea aphids are frequently attacked by a range of endoparasitic wasps, including the common aphidiine, aphidius ervi. immunity to parasitoid attack is thought to involve secondary symbiotic bacteria, the presence of which is associated with the death of the parasitoid egg. it has been suggested that there is a ...	2005	16096092
bacterial genome size reduction by experimental evolution.	bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. here we examined the rate and process of genome reduction in the bacterium salmonella enterica by a serial passage experimental evolution procedure. the initial rate of dna loss was estimated to be 0.05 bp per chromosome per generation for a wt bacterium and approximately 50-fold higher for a muts mutant defective in methyl-dire ...	2005	16099836
a stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization.	we have determined the effect of mutations involving isoleucine and valine (i.e., mutations i-->v and v-->i) on the stability of escherichia coli thioredoxin. despite the similarity in chemical structure (v and i differ only in a methyl group), we find that many environments are optimized to a significant extent for either v or i. we find, furthermore, that a plot of effect of hydrophobic mutations on stability versus packing density shows a strikingly simple pattern that clearly reflects evolut ...	2005	16100262
genomes on the shrink.		2005	16105941
e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects.	the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ...	2005	16109942
chromosomal stasis versus plasmid plasticity in aphid endosymbiont buchnera aphidicola.	the study of three genomes of the aphid endosymbiont buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. the reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first b. aphidicola analysed. the current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and ...	2005	16118664
genomes are covered with ubiquitous 11 bp periodic patterns, the "class a flexible patterns".	the genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. this bias is present throughout a given genome, both in coding and non-coding sequences. until now this bias remained of unknown origin.	2005	16120222
variation in resistance to parasitism in aphids is due to symbionts not host genotype.	natural enemies are important ecological and evolutionary forces, and heritable variation in resistance to enemies is a prerequisite for adaptive responses of populations. such variation in resistance has been previously documented for pea aphids (acyrthosiphon pisum) attacked by the parasitoid wasp aphidius ervi. although the variation was presumed to reflect genotypic differences among the aphids, another potential source of resistance to a. ervi is infection by the facultative bacterial symbi ...	2005	16120675