| a novel type of uracil-dna glycosylase mediating repair of hydrolytic dna damage in the extremely thermophilic eubacterium thermus thermophilus. | spontaneous hydrolytic deamination of dna cytosine and 5-methyl-cytosine residues is an abundant source of c/g (5-mec/g) to t/a transition mutations. as a result of this pressure, at least six different families of enzymes have evolved that initiate repair at u/g (t/g) mispairs, the relevant pre-mutagenic intermediates. the necessarily higher rate of the process at elevated temperatures must pose a correspondingly accentuated problem to contemporary thermophilic organisms and may have been a ser ... | 2002 | 12000829 |
| noti passporting to identify species composition of complex microbial systems. | we describe here a new method for large-scale scanning of microbial genomes on a quantitative and qualitative basis. to achieve this aim we propose to create noti passports: databases containing noti tags. we demonstrated that these tags comprising 19 bp of sequence information could be successfully generated using dna isolated from intestinal or fecal samples. such noti passports allow the discrimination between closely related bacterial species and even strains. this procedure for generating r ... | 2003 | 12527794 |
| origin of the 2-amino-2-deoxy-gluconate unit in rhizobium leguminosarum lipid a. expression cloning of the outer membrane oxidase lpxq. | an unusual feature of the lipid a from the plant endosymbionts rhizobium etli and rhizobium leguminosarum is the presence of a proximal sugar unit consisting of a 2-amino-2-deoxy-gluconate moiety in place of glucosamine. an outer membrane oxidase that generates the 2-amino-2-deoxy-gluconate unit from a glucosamine-containing precursor is present in membranes of r. leguminosarum and r. etli but not in s. meliloti or escherichia coli. we now report the identification of a hybrid cosmid that direct ... | 2003 | 12531908 |
| comparative analyses of the complete genome sequences of pierce's disease and citrus variegated chlorosis strains of xylella fastidiosa. | xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. x. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the american continent, and induces diverse disease phenotypes. previous molecular analyses indicated three distinct groups of x. fastidiosa isolates that were expected to be genetically divergent. here we r ... | 2003 | 12533478 |
| traffic at the tmrna gene. | a partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmrna gene (ssra) than for any type of trna gene. horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. diverse elements use ssra; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssra, and almost every s ... | 2003 | 12533482 |
| prediction and overview of the rpon-regulon in closely related species of the rhizobiales. | in the rhizobia, a group of symbiotic gram-negative soil bacteria, rpon (sigma54, sigman, ntra) is best known as the sigma factor enabling transcription of the nitrogen fixation genes. recent reports, however, demonstrate the involvement of rpon in other symbiotic functions, although no large-scale effort has yet been undertaken to unravel the rpon-regulon in rhizobia. we screened two complete rhizobial genomes (mesorhizobium loti, sinorhizobium meliloti) and four symbiotic regions (rhizobium et ... | 2002 | 12537565 |
| purification, molecular cloning, and characterization of pyridoxine 4-oxidase from microbacterium luteolum. | pyridoxine 4-oxidase (ec 1.1.3.12, pn 4-oxidase), which catalyzes the oxidation of pn by oxygen or other hydrogen acceptors to form pyridoxal and hydrogen peroxide or reduced forms of the acceptors, respectively, was purified for the first time to homogeneity from microbacterium luteolum yk-1 (=aureobacterium luteolum yk-1). the purified enzyme required fad for its catalytic activity and stability. the enzyme was a monomeric protein with the subunit molecular mass of 53,000 +/- 1,000 da. pn was ... | 2002 | 12092811 |
| biosynthesis of phosphatidylcholine in bacteria. | phosphatidylcholine (pc) is the major membrane-forming phospholipid in eukaryotes and can be synthesized by either of two pathways, the methylation pathway or the cdp-choline pathway. many prokaryotes lack pc, but it can be found in significant amounts in membranes of rather diverse bacteria and based on genomic data, we estimate that more than 10% of all bacteria possess pc. enzymatic methylation of phosphatidylethanolamine via the methylation pathway was thought to be the only biosynthetic pat ... | 2003 | 12547654 |
| genomic and functional analyses of sxt, an integrating antibiotic resistance gene transfer element derived from vibrio cholerae. | sxt is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. in recent years, sxt-related conjugative, self-transmissible integrating elements have become widespread in asian vibrio cholerae. we have determined the 100-kb dna sequence of sxt. this element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many gene ... | 2002 | 12107144 |
| prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey. | the twin-arginine translocation (tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. however, the extent to which this pathway is used among the prokaryotes is not known. by using a genomic approach, a comprehensive list of putative tat substrates for 84 diverse prokaryotes was established. strikingly, the results indicate that the tat pathway is utilized to highly varying extents. furthermore, while many prokaryotes use thi ... | 2003 | 12562823 |
| identification of klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis. | klebsiella pneumoniae is an opportunistic pathogen responsible for nosocomial infections that initially colonize the intestinal tract of patients. signature-tagged mutagenesis was used to identify genes required for this function. a library of 2,200 mutants was analyzed for the inability of the mutants to survive in a murine model of intestinal colonization and to adhere to human intestinal cells (int-407) in vitro. twenty-nine attenuated mutants were selected for further analyses after competit ... | 2002 | 12117993 |
| suppressive subtractive hybridization detects extensive genomic diversity in thermotoga maritima. | comparisons between genomes of closely related bacteria often show large variations in gene content, even between strains of the same species. such studies have focused mainly on pathogens; here, we examined thermotoga maritima, a free-living hyperthermophilic bacterium, by using suppressive subtractive hybridization. the genome sequence of t. maritima msb8 is available, and dna from this strain served as a reference to obtain strain-specific sequences from thermotoga sp. strain rq2, a very clos ... | 2002 | 12142418 |
| functional annotation of class i lysyl-trna synthetase phylogeny indicates a limited role for gene transfer. | functional and comparative genomic studies have previously shown that the essential protein lysyl-trna synthetase (lysrs) exists in two unrelated forms. most prokaryotes and all eukaryotes contain a class ii lysrs, whereas most archaea and a few bacteria contain a less common class i lysrs. in bacteria the class i lysrs is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class i protein is by far the most common form of lysrs in archae ... | 2002 | 12142429 |
| complete genomic sequence of nitrogen-fixing symbiotic bacterium bradyrhizobium japonicum usda110. | the complete nucleotide sequence of the genome of a symbiotic bacterium bradyrhizobium japonicum usda110 was determined. the genome of b. japonicum was a single circular chromosome 9,105,828 bp in length with an average gc content of 64.1%. no plasmid was detected. the chromosome comprises 8317 potential protein-coding genes, one set of rrna genes and 50 trna genes. fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical gene ... | 2002 | 12597275 |
| the pair of bacteriophytochromes from agrobacterium tumefaciens are histidine kinases with opposing photobiological properties. | bacteriophytochrome photoreceptors (bphps) are a family of phytochrome-like sensor kinases that help a wide variety of bacteria respond to their light environment. in agrobacterium tumefaciens, a unique pair of bphps with potentially opposing roles in light sensing are present. both atbphps contain an n-terminal chromophore-binding domain that covalently attaches a biliverdin chromophore. whereas atbphp1 assumes a pr ground state, atbphp2 is unusual in that it assumes a pfr ground state that is ... | 2003 | 12604773 |
| a rhizobium leguminosarum acpxl mutant produces lipopolysaccharide lacking 27-hydroxyoctacosanoic acid. | the structure of the lipid a from rhizobium etli and rhizobium leguminosarum lipopolysaccharides (lpss) lacks phosphate and contains a galacturonosyl residue at its 4' position, an acylated 2-aminogluconate in place of the proximal glucosamine, and a very long chain omega-1 hydroxy fatty acid, 27-hydroxyoctacosanoic acid (27ohc28:0). the 27ohc28:0 moiety is common in lipid a's among members of the rhizobiaceae and also among a number of the facultative intracellular pathogens that form chronic i ... | 2003 | 12618448 |
| the rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. | the rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. they are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. on the basis of experimental studies with the developmental regulator rhomboid from drosophila and the aara protein from the bacterium providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose ... | 2003 | 12620104 |
| lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in xylella species and in heterocystous cyanobacteria. | tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. a seven-gene cluster in xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-coa synthetase, and trpr. a second gene block, present in the anabaena/nostoc lineage, but not in other cyanobacteria, contains a near ... | 2003 | 12620124 |
| transcriptome analysis of sinorhizobium meliloti during symbiosis. | rhizobia induce the formation on specific legumes of new organs, the root nodules, as a result of an elaborated developmental program involving the two partners. in order to contribute to a more global view of the genetics underlying this plant-microbe symbiosis, we have mined the recently determined sinorhizobium meliloti genome sequence for genes potentially relevant to symbiosis. we describe here the construction and use of dedicated nylon macroarrays to study simultaneously the expression of ... | 2003 | 12620125 |
| construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on escherichia coli. | enrichment of microorganisms with special traits and the construction of metagenomic libraries by direct cloning of environmental dna have great potential for identifying genes and gene products for biotechnological purposes. we have combined these techniques to isolate novel genes conferring oxidation of short-chain (c(2) to c(4)) polyols or reduction of the corresponding carbonyls. in order to favor the growth of microorganisms containing the targeted genes, samples collected from four differe ... | 2003 | 12620823 |
| plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by terrabacter sp. strain yk3. | the genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of pcr primers designed by using conserved sequences of the dioxygenase alpha subunit genes. one sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: terrabacter sp. strains yk1 and yk3, rhodococcus sp. strain yk2, and microbacterium sp. strain yk18. a 5.2-kb psti fragment encoding the alpha and beta subunits of the terminal diox ... | 2002 | 12147464 |
| two families of mechanosensitive channel proteins. | mechanosensitive (ms) channels that provide protection against hypoosmotic shock are found in the membranes of organisms from the three domains of life: bacteria, archaea, and eucarya. two families of ubiquitous ms channels are recognized, and these have been designated the mscl and mscs families. a high-resolution x-ray crystallographic structure is available for a member of the mscl family, and extensive molecular genetic, biophysical, and biochemical studies conducted in many laboratories hav ... | 2003 | 12626684 |
| crinkle, a novel symbiotic mutant that affects the infection thread growth and alters the root hair, trichome, and seed development in lotus japonicus. | to elucidate the mechanisms involved in rhizobium-legume symbiosis, we examined a novel symbiotic mutant, crinkle (ljsym79), from the model legume lotus japonicus. on nitrogen-starved medium, crinkle mutants inoculated with the symbiont bacterium mesorhizobium loti maff 303099 showed severe nitrogen deficiency symptoms. this mutant was characterized by the production of many bumps and small, white, uninfected nodule-like structures. few nodules were pale-pink and irregularly shaped with nitrogen ... | 2003 | 12644658 |
| identification of a third sulfate activation system in sinorhizobium sp. strain br816: the cysdn sulfate activation complex. | sinorhizobium sp. strain br816 possesses two nodpq copies, providing activated sulfate (3'-phosphoadenosine-5'-phosphosulfate [paps]) needed for the biosynthesis of sulfated nod factors. it was previously shown that the nod factors synthesized by a nodpq double mutant are not structurally different from those of the wild-type strain. in this study, we describe the characterization of a third sulfate activation locus. two open reading frames were fully characterized and displayed the highest simi ... | 2003 | 12676676 |
| 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 |
| use of in-biofilm expression technology to identify genes involved in pseudomonas aeruginosa biofilm development. | mature pseudomonas aeruginosa biofilms form complex three-dimensional architecture and are tolerant of antibiotics and other antimicrobial compounds. in this work, an in vivo expression technology system, originally designed to study virulence-associated genes in complex mammalian environments, was used to identify genes up-regulated in p. aeruginosa grown to a mature (5-day) biofilm. five unique cloned promoters unable to promote in vitro growth in the absence of purines after recovery from the ... | 2003 | 12700249 |
| identification in methicillin-susceptible staphylococcus hominis of an active primordial mobile genetic element for the staphylococcal cassette chromosome mec of methicillin-resistant staphylococcus aureus. | we previously reported that the methicillin resistance gene meca is carried by a novel type of mobile genetic element, sccmec (staphylococcal cassette chromosome mec), in the chromosome of methicillin-resistant staphylococcus aureus (mrsa). these elements are precisely excised from the chromosome and integrated into a specific site on the recipient chromosome by a pair of recombinase proteins encoded by the cassette chromosome recombinase genes ccra and ccrb. in the present work, we detected hom ... | 2003 | 12700250 |
| complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph nitrosomonas europaea. | nitrosomonas europaea (atcc 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. nitrosomonas europaea participates in the biogeochemical n cycle in the process of nitrification. its genome consists of a single circular chromosome of 2,812,094 bp. the gc skew analysis indicates that the genome is divided into two unequal replichores. genes are distributed evenly around the genome, with approximate ... | 2003 | 12700255 |
| atypical 16s rrna gene copies in ochrobactrum intermedium strains reveal a large genomic rearrangement by recombination between rrn copies. | ochrobactrum intermedium is an opportunistic human pathogen belonging to the alpha 2 subgroup of proteobacteria. the 16s rdna sequences of nine o. intermedium isolates from a collection of clinical and environmental isolates exhibited a 46-bp insertion at position 187, which was present in only one sequence among the 82 complete or partial 16s rdna sequences of ochrobactrum spp. available in data banks. reverse transcription-pcr experiments showed that the 46-bp insertion remained in the 16s rrn ... | 2003 | 12700269 |
| cloning and expression of the haloalkane dehalogenase gene dhma from mycobacterium avium n85 and preliminary characterization of dhma. | haloalkane dehalogenases are microbial enzymes that catalyze cleavage of the carbon-halogen bond by a hydrolytic mechanism. until recently, these enzymes have been isolated only from bacteria living in contaminated environments. in this report we describe cloning of the dehalogenase gene dhma from mycobacterium avium subsp. avium n85 isolated from swine mesenteric lymph nodes. the dhma gene has a g+c content of 68.21% and codes for a polypeptide that is 301 amino acids long and has a calculated ... | 2002 | 12147465 |
| temperature-regulated transcription in the pathogenic fungus cryptococcus neoformans. | the basidiomycete fungus cryptococcus neoformans is an opportunistic pathogen of worldwide importance that causes meningitis, leading to death in immunocompromised individuals. unlike many basidiomycete fungi, c. neoformans is thermotolerant, and its ability to grow at 37 degrees c is considered to be a virulence factor. we used serial analysis of gene expression (sage) to characterize the transcriptomes of c. neoformans strains that represent two varieties with different polysaccharide capsule ... | 2002 | 12213776 |
| discordant phylogenies within the rrn loci of rhizobia. | it is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-proteobacteria by sequencing analysis of three loci within their rrn operons. tree topologies generated with 16s rrna gene sequences were ... | 2003 | 12730157 |
| wavelet to predict bacterial ori and ter: a tendency towards a physical balance. | chromosomal dna replication in bacteria starts at the origin (ori) and the two replicores propagate in opposite directions up to the terminus (ter) region. we hypothesize that the two replicores need to reach ter at the same time to maintain a physical balance; dna insertion would disrupt such a balance, requiring chromosomal rearrangements to restore the balance. to test this hypothesis, we needed to demonstrate that ori and ter are in a physical balance in bacterial chromosomes. using wavelet ... | 2003 | 12732098 |
| genomics insights into symbiotic nitrogen fixation. | following an interaction with rhizobial soil bacteria, legume plants are able to form a novel organ, termed the root nodule. this organ houses the rhizobial microsymbionts, which perform the biological nitrogen fixation process resulting in the incorporation of ammonia into plant organic molecules. recent advances in genomics have opened exciting new perspectives in this field by providing the complete gene inventory of two rhizobial microsymbionts. the complete genome sequences of mesorhizobium ... | 2003 | 12732321 |
| purification, substrate range, and metal center of atzc: the n-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. | n-isopropylammelide isopropylaminohydrolase, atzc, the third enzyme in the atrazine degradation pathway in pseudomonas sp. strain adp, catalyzes the stoichiometric hydrolysis of n-isopropylammelide to cyanuric acid and isopropylamine. the atzc gene was cloned downstream of the tac promoter and expressed in escherichia coli, where the expressed enzyme comprised 36% of the soluble protein. atzc was purified to homogeneity by ammonium sulfate precipitation and phenyl column chromatography. it has a ... | 2002 | 12218024 |
| distribution and organization of auxotrophic genes on the multichromosomal genome of burkholderia multivorans atcc 17616. | the burkholderia multivorans strain atcc 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 mb. to determine the distribution and organization of the amino acid biosynthetic genes on the genome of this beta-proteobacterium, various auxotrophic mutations were isolated using a tn5 derivative that was convenient not only for the determination of its insertion site on the genome map but also for the structural analysis of the flanking regions. analysis by pulsed-field gel elect ... | 2003 | 12754231 |
| the dithiol:disulfide oxidoreductases dsba and dsbb of rhodobacter capsulatus are not directly involved in cytochrome c biogenesis, but their inactivation restores the cytochrome c biogenesis defect of ccda-null mutants. | the cytoplasmic membrane protein ccda and its homologues in other species, such as dsbd of escherichia coli, are thought to supply the reducing equivalents required for the biogenesis of c-type cytochromes that occurs in the periplasm of gram-negative bacteria. ccda-null mutants of the facultative phototroph rhodobacter capsulatus are unable to grow under photosynthetic conditions (ps(-)) and do not produce any active cytochrome c oxidase (nadi(-)) due to a pleiotropic cytochrome c deficiency. h ... | 2003 | 12754234 |
| effect of omp10 or omp19 deletion on brucella abortus outer membrane properties and virulence in mice. | the distinctive properties of brucella outer membrane have been considered to be critical for brucella sp. virulence. among the outer membrane molecules possibly related to these properties, omp10 and omp19 are immunoreactive outer membrane lipoproteins. moreover, these proteins of brucella could constitute a new family of outer membrane proteins specifically encountered in the family rhizobiaceae: we evaluated the impact of omp10 or omp19 deletion on brucella abortus outer membrane properties a ... | 2002 | 12228280 |
| predicting gene expression levels from codon biases in alpha-proteobacterial genomes. | predicted highly expressed (phx) genes in five currently available high g+c complete alpha-proteobacterial genomes are analyzed. these include: the nitrogen-fixing plant symbionts sinorhizobium meliloti (sinme) and mesorhizobium loti (meslo), the nonpathogenic aquatic bacterium caulobacter crescentus (caucr), the plant pathogen agrobacterium tumefaciens (agrtu), and the mammalian pathogen brucella melitensis (brume). three of these genomes, sinme, agrtu, and brume, contain multiple chromosomes o ... | 2003 | 12775761 |
| the mosaic structure of the symbiotic plasmid of rhizobium etli cfn42 and its relation to other symbiotic genome compartments. | symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. in rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. to understand the structure and evolution of the symbiotic genome compartments (sgcs), it is necessary to analyze their common genetic content and organization as well as to study their differences. to date, five sgcs belonging to distinct spec ... | 2003 | 12801410 |
| identification and characterization of transposable elements of paracoccus pantotrophus. | we studied diversity and distribution of transposable elements residing in different strains (dsm 11072, dsm 11073, dsm 65, and lmd 82.5) of a soil bacterium paracoccus pantotrophus (alpha-proteobacteria). with application of a shuttle entrapment vector pmec1, several novel insertion sequences (iss) and transposons (tns) have been identified. they were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, termin ... | 2003 | 12813068 |
| striking complexity of lipopolysaccharide defects in a collection of sinorhizobium meliloti mutants. | although the role that lipopolysaccharide (lps) plays in the symbiosis between sinorhizobium meliloti and alfalfa has been studied for over a decade, its function in this process remains controversial and poorly understood. this is largely due to a lack of mutants affected by its synthesis. in one of the definitive studies concerning this issue, clover et al. (r. h. clover, j. kieber, and e. r. signer, j. bacteriol. 171:3961-3967, 1989) identified a series of mutants with putative lps defects, j ... | 2003 | 12813079 |
| distribution and evolution of von willebrand/integrin a domains: widely dispersed domains with roles in cell adhesion and elsewhere. | the von willebrand a (vwa) domain is a well-studied domain involved in cell adhesion, in extracellular matrix proteins, and in integrin receptors. a number of human diseases arise from mutations in vwa domains. we have analyzed the phylogenetic distribution of this domain and the relationships among approximately 500 proteins containing this domain. although the majority of vwa-containing proteins are extracellular, the most ancient ones, present in all eukaryotes, are all intracellular proteins ... | 2002 | 12388743 |
| biochemistry and comparative genomics of sxxk superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent. | the bacterial acyltransferases of the sxxk superfamily vary enormously in sequence and function, with conservation of particular amino acid groups and all-alpha and alpha/beta folds. they occur as independent entities (free-standing polypeptides) and as modules linked to other polypeptides (protein fusions). they can be classified into three groups. the group i sxxk d,d-acyltransferases are ubiquitous in the bacterial world. they invariably bear the motifs sxxk, sxn(d), and kt(s)g. anchored in t ... | 2002 | 12456788 |
| mutational and transcriptional analysis of the type iii secretion system of bradyrhizobium japonicum. | sequencing the symbiotic region of bradyrhizobium japonicum revealed a gene cluster (tts) encoding a type iii secretion system (ttss) that is similar to those found in mesorhizobium loti maff303099 and rhizobium strain ngr234. in addition to genes that are likely to encode structural core components of the ttss, the cluster contains several open reading frames that are found exclusively in rhizobia or that are specific to b. japonicum. depending on the host, mutations within this cluster affecte ... | 2002 | 12481995 |
| molecular characterization and expression in escherichia coli of three beta-1,3-glucanase genes from lysobacter enzymogenes strain n4-7. | lysobacter enzymogenes strain n4-7 produces multiple biochemically distinct extracellular beta-1,3-glucanase activities. the glua, glub, and gluc genes, encoding enzymes with beta-1,3-glucanase activity, were identified by a reverse-genetics approach following internal amino acid sequence determination of beta-1,3-glucanase-active proteins partially purified from culture filtrates of strain n4-7. analysis of glua and gluc gene products indicates that they are members of family 16 glycoside hydro ... | 2003 | 12867444 |
| expression cloning and biochemical characterization of a rhizobium leguminosarum lipid a 1-phosphatase. | lipid a of rhizobium leguminosarum, a nitrogen-fixing plant endosymbiont, displays several significant structural differences when compared with escherichia coli. an especially striking feature of r. leguminosarum lipid a is that it lacks both the 1- and 4'-phosphate groups. distinct lipid a phosphatases that attack either the 1 or the 4' positions have previously been identified in extracts of r. leguminosarum and rhizobium etli but not sinorhizobium meliloti or e. coli. here we describe the id ... | 2003 | 12869541 |
| molecular characterization of the sucb gene encoding the immunogenic dihydrolipoamide succinyltransferase protein of bartonella vinsonii subsp. berkhoffii and bartonella quintana. | members of the genus bartonella have historically been connected with human disease, such as cat scratch disease, trench fever, and carrion's disease, and recently have been recognized as emerging pathogens causing other clinical manifestations in humans. however, because little is known about the antigens that elicit antibody production in response to bartonella infections, this project was undertaken to identify and molecularly characterize these immunogens. immunologic screening of a bartonel ... | 2003 | 12874367 |
| identification of long intergenic repeat sequences associated with dna methylation sites in caulobacter crescentus and other alpha-proteobacteria. | a systematic search for motifs associated with ccrm dna methylation sites revealed four long (>100-bp) motifs (cir sequences) present in up to 21 copies in caulobacter crescentus. the cir1 and cir2 motifs exhibit a conserved inverted repeat organization, with a ccrm site in the center of one of the repeats. | 2003 | 12897020 |
| rhizobium leguminosarum biovar viciae 1-aminocyclopropane-1-carboxylate deaminase promotes nodulation of pea plants. | ethylene inhibits nodulation in various legumes. in order to investigate strategies employed by rhizobium to regulate nodulation, the 1-aminocyclopropane-1-carboxylate (acc) deaminase gene was isolated and characterized from one of the acc deaminase-producing rhizobia, rhizobium leguminosarum bv. viciae 128c53k. acc deaminase degrades acc, the immediate precursor of ethylene in higher plants. through the action of this enzyme, acc deaminase-containing bacteria can reduce ethylene biosynthesis in ... | 2003 | 12902221 |
| domain organization of the mscs mechanosensitive channel of escherichia coli. | the major structural features of the escherichia coli mscs mechanosensitive channel protein have been explored using alkaline phosphatase (phoa) fusions, precise deletions and site-directed mutations. phoa protein fusion data, combined with the positive-inside rule, strongly support a model in which mscs crosses the membrane three times, adopting an n(out)-c(in) configuration. deletion data suggest that the c-terminal domain of the protein is essential for the stability of the mscs channel, wher ... | 2003 | 12505982 |
| the ti plasmid of agrobacterium tumefaciens harbors an attm-paralogous gene, aiib, also encoding n-acyl homoserine lactonase activity. | the agrobacterium tumefaciens c58 genome contains three putative n-acyl homoserine lactone (acyl-hsl) hydrolases, which are closely related to the lactonase aiia of bacillus. when expressed in escherichia coli, two of the putative acyl-hsl hydrolases, attm and aiib, conferred the ability to degrade acyl-hsls on the host. in erwinia strain 6276, the lactonases reduced the endogenous acyl-hsl level and the bacterial virulence in planta. | 2003 | 12902298 |
| comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. | zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. thus its transport is regulated by zinc repressors zur of proteobacteria and gram-positive bacteria from the bacillus group and adcr of bacteria from the streptococcus group. comparative computational analysis allowed us to identify binding signals of zur repressors gaaatgttatantataacatttc for gamma-proteobacteria, gtaatgtaataacattac for the agrobacterium group, gatatgttataacatatc for the rh ... | 2003 | 12904577 |
| application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. | a great diversity of multi-pass membrane receptors, typically with 7 transmembrane (tm) helices, is observed in the eukaryote crown group. so far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes. | 2003 | 12914674 |
| control of sxt integration and excision. | the vibrio cholerae sxt element is a conjugative self-transmissible chromosomally integrating element that encodes resistance to multiple antibiotics. sxt integrates in a site-specific fashion at prfc and excises from the chromosome to form a circular but nonreplicative extrachromosomal form. both chromosomal integration and excision depend on an sxt-encoded recombinase, int. here we found that int is necessary and sufficient for sxt integration and that int expression in recipient cells require ... | 2003 | 12923077 |
| the structure of actva-orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis. | actva-orf6 monooxygenase from streptomyces coelicolor that catalyses the oxidation of an aromatic intermediate of the actinorhodin biosynthetic pathway is a member of a class of small monooxygenases that carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. the overall structure is a ferredoxin-like fold with a novel dimeric assembly, indicating that the widely represented ferredoxin fold may ... | 2003 | 12514126 |
| regulation of the vitamin b12 metabolism and transport in bacteria by a conserved rna structural element. | cobalamin in the form of adenosylcobalamin (ado-cbl) is known to repress expression of genes for vitamin b(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding of ado-cbl to 5'untranslated gene regions (5'utr). using comparative analysis of genes and regulatory regions, we identified a highly conserved rna structure, the b12-element, which is widely distributed in 5'utrs of vitamin b(12)-related genes in eubacteria. multiple alignment o ... | 2003 | 12923257 |
| ordered cosmid library of the mesorhizobium loti maff303099 genome for systematic gene disruption and complementation analysis. | for effective exploitation of the genome sequence information of lotus microsymbiont, mesorhizobium loti maff303099, to discover gene functions, we have constructed an ordered and mutually overlapping cosmid library using an incp broad host-range vector. the library consisted of 480 clones to cover approximately 99.6% of the genome with average insert size and overlap of 26.9 and 11.1 kbp, respectively. the genome of m. loti consists of a single chromosome and two plasmids. the chromosome (7,036 ... | 2002 | 12514252 |
| algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. | comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (hgt), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. this complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. | 2003 | 12515582 |
| 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 |
| whole-genome sequence variation among multiple isolates of pseudomonas aeruginosa. | whole-genome shotgun sequencing was used to study the sequence variation of three pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain pao1. the majority of the pao1 genome is represented in these strains; however, at least three prominent islands of pao1-specific sequence are apparent. conversely, approximately 10% of the sequencing reads derived from each isolate fail to ... | 2003 | 12562802 |
| purification and characterization of an immunogenic aminopeptidase of brucella melitensis. | an immunogenic aminopeptidase was purified from brucella melitensis strain vtrm1. the purification procedure consisted of ammonium sulfate fractionation and three chromatographic steps. this procedure resulted in a yield of 29% and a 144-fold increase in specific activity. the aminopeptidase appeared to be a monomeric enzyme with a molecular mass of 96 kda and an isoelectric point of 4.8. its activity was optimal at ph 7.0 at 40 degrees c. the enzyme was strongly inhibited by edta, 1,10-phenathr ... | 2003 | 12933870 |
| ehrlichia chaffeensis and anaplasma phagocytophilum lack genes for lipid a biosynthesis and incorporate cholesterol for their survival. | ehrlichia chaffeensis and anaplasma phagocytophilum are agents of human monocytic and granulocytic ehrlichioses, respectively. they are extremely sensitive to mechanical stress and are pleomorphic gram-negative bacteria. membrane incorporation of cholesterol from the eukaryotic host is known to be essential for other fragile and pleomorphic bacteria and mycoplasmas that lack a cell wall. thus, we tested whether cholesterol is required for e. chaffeensis and a. phagocytophilum. using a freeze fra ... | 2003 | 12933880 |
| evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. | shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire opero ... | 2003 | 12952534 |
| the cog database: an updated version includes eukaryotes. | the availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. | 2003 | 12969510 |
| genome sequence survey identifies unique sequences and key virulence genes with unusual rates of amino acid substitution in bovine staphylococcus aureus. | staphylococcus aureus is a major cause of mastitis in bovine and other ruminant species. we here present the results of a comparative genomic analysis between a bovine mastitis-associated clone, rf122, and the recently sequenced human-associated clones, mu50 and n315, of staphylococcus aureus. a shotgun sequence survey of approximately 10% of the rf122 genome identified numerous unique sequences and those with elevated rates of nonsynonymous substitution. taken together, these analyses show that ... | 2002 | 12065548 |
| gw domains of the listeria monocytogenes invasion protein inlb are sh3-like and mediate binding to host ligands. | inlb, a surface-localized protein of listeria monocytogenes, induces phagocytosis in non-phagocytic mammalian cells by activating met, a receptor tyrosine kinase. inlb also binds glycosaminoglycans and the protein gc1q-r, two additional host ligands implicated in invasion. we present the structure of inlb, revealing a highly elongated molecule with leucine-rich repeats that bind met at one end, and gw domains that dissociably bind the bacterial surface at the other. surprisingly, the gw domains ... | 2002 | 12411480 |
| a key role for old yellow enzyme in the metabolism of drugs by trypanosoma cruzi. | trypanosoma cruzi is the etiological agent of chagas' disease. so far, first choice anti-chagasic drugs in use have been shown to have undesirable side effects in addition to the emergence of parasite resistance and the lack of prospect for vaccine against t. cruzi infection. thus, the isolation and characterization of molecules essential in parasite metabolism of the anti-chagasic drugs are fundamental for the development of new strategies for rational drug design and/or the improvement of the ... | 2002 | 12417633 |
| what does a bacterial genome sequence represent? mis-assignment of maff 303099 to the genospecies mesorhizobium loti. | | 2002 | 12427922 |
| characterization of two noncellulosomal subunits, arfa and bgaa, from clostridium cellulovorans that cooperate with the cellulosome in plant cell wall degradation. | plant cell wall degradation by clostridium cellulovorans requires the cooperative activity of its cellulases and hemicellulases. to characterize the alpha-l-arabinosidases that are involved in hemicellulose degradation, we screened the c. cellulovorans genomic library for clones with alpha-l-arabinofuranosidase or alpha-l-arabinopyranosidase activity, and two clones utilizing different substrates were isolated. the genes from the two clones, arfa and bgaa, encoded proteins of 493 and 659 amino a ... | 2002 | 12446636 |
| molecular genetic analysis of icef, an integrative conjugal element that is present as a repetitive sequence in the chromosome of mycoplasma fermentans pg18. | mycoplasma genomes contain compact gene sets that approach the minimal complement necessary for life and reflect multiple evolutionary instances of genomic reduction. lateral gene transfer may play a critical role in shaping the mobile gene pool in these organisms, yet complex mobile elements have not been reported within this genus. we describe here a large ( approximately 23-kb) genetic element with unique features that is present in four copies in the mycoplasma fermentans pg18 chromosome, ac ... | 2002 | 12446643 |
| a glutamate mutase is involved in the biosynthesis of the lipopeptide antibiotic friulimicin in actinoplanes friuliensis. | actinoplanes friuliensis produces the lipopeptide antibiotic friulimicin. this antibiotic is active against gram-positive bacteria such as multiresistant enterococcus and staphylococcus strains. it consists of 10 amino acids that form a ring structure and 1 exocyclic amino acid to which an acyl residue is attached. by a reverse genetic approach, biosynthetic genes were identified that are required for the nonribosomal synthesis of the antibiotic. in close proximity two genes (glma and glmb) were ... | 2003 | 12543643 |
| characterization of a thermostable d-stereospecific alanine amidase from brevibacillus borstelensis bcs-1. | a gene encoding a new thermostable d-stereospecific alanine amidase from the thermophile brevibacillus borstelensis bcs-1 was cloned and sequenced. the molecular mass of the purified enzyme was estimated to be 199 kda after gel filtration chromatography and about 30 kda on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that the enzyme could be composed of a hexamer with identical subunits. the purified enzyme exhibited strong amidase activity towards d-amino acid-containin ... | 2003 | 12571020 |
| salicylic acid inhibits indeterminate-type nodulation but not determinate-type nodulation. | lcos (lipochitin oligosaccharides, nod factors) produced by the rhizobial symbiote of vicia sativa subsp. nigra (vetch, an indeterminate-type nodulating plant) are mitogenic when carrying an 18:4 acyl chain but not when carrying an 18:1 acyl chain. this suggests that the 18:4 acyl chain specifically contributes to signaling in indeterminate-type nodulation. in a working hypothesis, we speculated that the 18:4 acyl chain is involved in oxylipin signaling comparable to, for example, signaling by d ... | 2003 | 12580285 |
| a mannosyl transferase required for lipopolysaccharide inner core assembly in rhizobium leguminosarum. purification, substrate specificity, and expression in salmonella waac mutants. | the lipopolysaccharide (lps) core domain of gram-negative bacteria plays an important role in outer membrane stability and host interactions. little is known about the biochemical properties of the glycosyltransferases that assemble the lps core. we now report the purification and characterization of the rhizobium leguminosarum mannosyl transferase lpcc, which adds a mannose unit to the inner 3-deoxy-d-manno-octulosonic acid (kdo) moiety of the lps precursor, kdo(2)-lipid iv(a). lpcc containing ... | 2003 | 12591937 |
| new knowledge from old: in silico discovery of novel protein domains in streptomyces coelicolor. | streptomyces coelicolor has long been considered a remarkable bacterium with a complex life-cycle, ubiquitous environmental distribution, linear chromosomes and plasmids, and a huge range of pharmaceutically useful secondary metabolites. completion of the genome sequence demonstrated that this diversity carried through to the genetic level, with over 7000 genes identified. we sought to expand our understanding of this organism at the molecular level through identification and annotation of novel ... | 2003 | 12625841 |
| complete genome sequence and comparative genomics of shigella flexneri serotype 2a strain 2457t. | we determined the complete genome sequence of shigella flexneri serotype 2a strain 2457t (4,599,354 bp). shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including escherichia coli. the genome exhibits the backbone and island mosaic structure of e. coli pathogens, albeit with much less horizontally transferred dna and lacking 357 genes present in e. coli. the strain is distinctive ... | 2003 | 12704152 |
| the enigmatic mitochondrial orf ymf39 codes for atp synthase chain b. | ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. we speculated earlier, based on a weak sequence similarity between ymf39 from a green alga and the atpf gene product from bradyrhizobium, that ymf39 might code for subunit b of mitochondrial f(0)f(1)-atp synthase. to test this hypothesis, we have sequenced ymf39 from five protists with minimally derived mitochondrial genomes, the jakobids. in addition, we isolated the mitocho ... | 2003 | 12711680 |
| microbial population diversity in the urethras of healthy males and males suffering from nonchlamydial, nongonococcal urethritis. | nonchlamydial, nongonococcal urethritis (ncngu) is suggested to be a sexually transmitted disease in men. ncngu patients were compared to control subjects with regard to the presence of potentially infectious bacteria in the first void urine. patients' pre- and post-antibiotic-treatment urine samples and two samples obtained 2 weeks apart from healthy volunteers, who did not receive antibiotic therapy, were analyzed with broad-spectrum pcr tests aiming at eubacterial small subunit rrna genes. re ... | 2003 | 12734237 |
| characterization of brucella abortus o-polysaccharide and core lipopolysaccharide mutants and demonstration that a complete core is required for rough vaccines to be efficient against brucella abortus and brucella ovis in the mouse model. | brucella abortus rough lipopolysaccharide (lps) mutants were obtained by transposon insertion into two wbk genes (wbka [putative glycosyltransferase; formerly rfbu] and per [perosamine synthetase]), into manb (pmm [phosphomannomutase; formerly rfbk]), and into an unassigned gene. consistent with gene-predicted roles, electrophoretic analysis, 2-keto-3-manno-d-octulosonate measurements, and immunoblots with monoclonal antibodies to o-polysaccharide, outer and inner core epitopes showed no o-polys ... | 2003 | 12761107 |
| susceptibility and adaptive response to bile salts in propionibacterium freudenreichii: physiological and proteomic analysis. | tolerance to digestive stresses is one of the main factors limiting the use of microorganisms as live probiotic agents. susceptibility to bile salts and tolerance acquisition in the probiotic strain propionibacterium freudenreichii si41 were characterized. we showed that pretreatment with a moderate concentration of bile salts (0.2 g/liter) greatly increased its survival during a subsequent lethal challenge (1.0 g/liter, 60 s). bile salts challenge led to drastic morphological changes, consisten ... | 2003 | 12839748 |
| the balance of driving forces during genome evolution in prokaryotes. | genomes are shaped by evolutionary processes such as gene genesis, horizontal gene transfer (hgt), and gene loss. to quantify the relative contributions of these processes, we analyze the distribution of 12,762 protein families on a phylogenetic tree, derived from entire genomes of 41 bacteria and 10 archaea. we show that gene loss is the most important factor in shaping genome content, being up to three times more frequent than hgt, followed by gene genesis, which may contribute up to twice as ... | 2003 | 12840037 |
| sm-like proteins in eubacteria: the crystal structure of the hfq protein from escherichia coli. | the hfq protein was discovered in escherichia coli in the early seventies as a host factor for the qbeta phage rna replication. during the last decade, it was shown to be involved in many rna processing events and remote sequence homology indicated a link to spliceosomal sm proteins. we report the crystal structure of the e.coli hfq protein showing that its monomer displays a characteristic sm-fold and forms a homo-hexamer, in agreement with former biochemical data. overall, the structure of the ... | 2003 | 12853626 |
| the biphenyl- and 4-chlorobiphenyl-catabolic transposon tn4371, a member of a new family of genomic islands related to incp and ti plasmids. | the nucleotide sequence of the biphenyl catabolic transposon tn4371 has been completed and analyzed. it confirmed that the element has a mosaic structure made of several building blocks. in addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of achromobacter georgiopolitanum kks102, tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, pl ... | 2003 | 12902278 |
| composition, acquisition, and distribution of the vi exopolysaccharide-encoding salmonella enterica pathogenicity island spi-7. | vi capsular polysaccharide production is encoded by the viab locus, which has a limited distribution in salmonella enterica serovars. in s. enterica serovar typhi, viab is encoded on a 134-kb pathogenicity island known as spi-7 that is located between partially duplicated trna(pheu) sites. functional and bioinformatic analysis suggests that spi-7 has a mosaic structure and may have evolved as a consequence of several independent insertion events. analysis of viab-associated dna in vi-positive s. ... | 2003 | 12923078 |
| a novel antimicrobial protein isolated from potato (solanum tuberosum) shares homology with an acid phosphatase. | the nucleotide and amino acids sequences for ap(1) will appear in the genbank(r) and ncbi databases under accession number ay297449. a novel antimicrobial protein (ap(1)) was purified from leaves of the potato ( solanum tuberosum, variety ms-42.3) with a procedure involving ammonium sulphate fractionation, molecular sieve chromatography with sephacryl s-200 and hydrophobic chromatography with butyl-sepharose using a fplc system. the inhibition spectrum investigation showed that ap(1) had good in ... | 2003 | 12927022 |
| intrinsic contributions of polar amino acid residues toward thermal stability of an abc-atpase of mesophilic origin. | the nucleotide-binding subunit of phosphate-specific transporter (pstb) from mesophilic bacterium, mycobacterium tuberculosis, is a unique atp-binding cassette (abc) atpase because of its unusual ability to hydrolyze atp at high temperature. in an attempt to define the basis of thermostability, we took a theoretical approach and compared amino acid composition of this protein to that of other pstbs from available bacterial genomes. interestingly, based on the content of polar amino acids, this p ... | 2003 | 12931011 |
| elucidation of the o-chain structure from the lipopolysaccharide of agrobacterium tumefaciens strain c58. | a linear homopolysaccharide built of 3-alpha-l-6dtalp residues, randomly acetylated at position c-4, is described for the o-specific polysaccharide of agrobacterium tumefaciens strain c58. this structure, determined by spectroscopical and chemical methods, is strictly correlated to that of rhizobium loti strain nzp2213, which differs for the degree and the position of o-acetylation. | 2003 | 12932373 |
| a lotus japonicus beta-type carbonic anhydrase gene expression pattern suggests distinct physiological roles during nodule development. | a full-length cdna clone, designated ljca1, coding for a beta-type carbonic anhydrase (ca; ec: 4.2.1.1) was isolated from a lotus japonicus nodule cdna library. semi-quantitative rt-pcr analysis revealed that ljca1 codes for a nodule-specific ca, transcripts of which accumulate at maximum levels in young nodules at 14 days post-infection (d.p.i.). in situ hybridization and immunolocalization revealed that ljca1 transcripts and ljca1 polypeptides were present at high levels in all cell types of y ... | 2003 | 12932831 |
| does lowering glutamine synthetase activity in nodules modify nitrogen metabolism and growth of lotus japonicus? | a cdna encoding cytosolic glutamine synthetase (gs) from lotus japonicus was fused in the antisense orientation relative to the nodule-specific lbc3 promoter of soybean (glycine max) and introduced into l. japonicus via transformation with agrobacterium tumefaciens. among the 12 independent transformed lines into which the construct was introduced, some of them showed diminished levels of gs1 mrna and lower levels of gs activity. three of these lines were selected and their t(1) progeny was furt ... | 2003 | 12970491 |
| experimental determination and system level analysis of essential genes in escherichia coli mg1655. | defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. we used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of escherichia coli in rich media. we identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. functional context analysis of these data allows individual functional assignment ... | 2003 | 13129938 |
| characterization of a spontaneous nonmagnetic mutant of magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island. | frequent spontaneous loss of the magnetic phenotype was observed in stationary-phase cultures of the magnetotactic bacterium magnetospirillum gryphiswaldense msr-1. a nonmagnetic mutant, designated strain msr-1b, was isolated and characterized. the mutant lacked any structures resembling magnetosome crystals as well as internal membrane vesicles. the growth of strain msr-1b was impaired under all growth conditions tested, and the uptake and accumulation of iron were drastically reduced under iro ... | 2003 | 13129949 |
| complete sequence of virulence plasmid pjm1 from the marine fish pathogen vibrio anguillarum strain 775. | the virulence plasmid pjm1 enables the fish pathogen vibrio anguillarum, a gram-negative polarly flagellated comma-shaped rod bacterium, to cause a highly fatal hemorrhagic septicemic disease in salmonids and other fishes, leading to epizootics throughout the world. the pjm1 plasmid 65,009-nucleotide sequence, with an overall g+c content of 42.6%, revealed genes and open reading frames (orfs) encoding iron transporters, nonribosomal peptide enzymes, and other proteins essential for the biosynthe ... | 2003 | 13129954 |
| a noncognate aminoacyl-trna synthetase that may resolve a missing link in protein evolution. | efforts to delineate the advent of many enzymes essential to protein translation are often limited by the fact that the modern genetic code evolved before divergence of the tree of life. glutaminyl-trna synthetase (glnrs) is one noteworthy exception to the universality of the translation apparatus. in eukaryotes and some bacteria, this enzyme is essential for the biosynthesis of gln-trnagln, an obligate intermediate in translation. glnrs is absent, however, in archaea, and most bacteria, organel ... | 2003 | 13679580 |
| isolation and molecular characterization of thiosulfate-oxidizing bacteria from an italian rice field soil. | in rice paddy soils an active cycling of sulfur compounds takes place. to elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. from the mpn enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. these strains were characterized by 16s rdna analyses. the isolates were affiliated to seven diffe ... | 2003 | 14529188 |
| lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of nepsilon-acetyl-beta-lysine and growth at high salinity. | the compatible solute n(epsilon)-acetyl-beta-lysine is unique to methanogenic archaea and is produced under salt stress only. however, the molecular basis for the salt-dependent regulation of n(epsilon)-acetyl-beta-lysine formation is unknown. genes potentially encoding lysine-2,3-aminomutase (abla) and beta-lysine acetyltransferase (ablb), which are assumed to catalyze n(epsilon)-acetyl-beta-lysine formation from alpha-lysine, were identified on the chromosomes of the methanogenic archaea metha ... | 2003 | 14532061 |
| low sequence similarity and gene content of symbiotic clusters of bradyrhizobium sp. wm9 (lupinus) indicate early divergence of "lupin" lineage in the genus bradyrhizobium. | two sequenced nodulation regions of lupin bradyrhizobium sp. wm9 carried the majority of genes involved in the nod factor production. the nod region i harbored: nola, nodd, noda, nodb, nodc, nods, nodi, nodj, nolo, nodz, fixr, nifa, fixa, nodm, nolk and noel. this gene arrangement resembled that found in the nodulation region of bradyrhizobium japonicum usda110, however strain wm9 harbored only one nodd gene copy, while the nodm, nolk and noel genes had no counterparts in the 410 kb symbiotic re ... | 2003 | 14533715 |
| plant recognition of symbiotic bacteria requires two lysm receptor-like kinases. | although most higher plants establish a symbiosis with arbuscular mycorrhizal fungi, symbiotic nitrogen fixation with rhizobia is a salient feature of legumes. despite this host range difference, mycorrhizal and rhizobial invasion shares a common plant-specified genetic programme controlling the early host interaction. one feature distinguishing legumes is their ability to perceive rhizobial-specific signal molecules. we describe here two lysm-type serine/threonine receptor kinase genes, nfr1 an ... | 2003 | 14534578 |
| d-xylose metabolism in hypocrea jecorina: loss of the xylitol dehydrogenase step can be partially compensated for by lad1-encoded l-arabinitol-4-dehydrogenase. | with the goal of the genetic characterization of the d-xylose pathway in hypocrea jecorina (anamorph: trichoderma reesei), we cloned the xdh1 gene, encoding nad-xylitol dehydrogenase, which catalyzes the second step of fungal d-xylose catabolism. this gene encodes a 363-amino-acid protein which has a mass of 38 kda, belongs to the zinc-containing alcohol dehydrogenase family, exhibits high sequence identity to the published sequences of xylitol dehydrogenases from yeast origins, but contains a s ... | 2003 | 14555469 |
| the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons. | is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ... | 2003 | 14563872 |