Publications

gene expression in chromobacterium violaceum.	the repertoire of 4,431 open reading frames (orfs), eight rrna operons and 98 trna genes of chromobacterium violaceum must be expressed in a regulated manner for successful adaptation to a wide variety of environmental conditions. to accomplish this feat, the organism relies on protein machineries involved in transcription, rna processing and translation. analysis of the c. violaceum genome showed that transcription initiation, elongation and termination are performed by the five well-known rna ...	2004	15100988
bacteriophages and insertion sequences of chromobacterium violaceum atcc 12472.	a fluid genome is a great advantage to prokaryotes, enabling quick adaptation to various types of ecological niches and to diverse environmental selective pressures. a substantial portion of these sudden changes is mediated by lateral gene transfer (lgt), through genetic recombination mechanisms, such as transformation, conjugation and transduction. the recent sequencing of several organisms has offered a new approach to the study of lgt, using comparison and analysis of nucleotide sequences dis ...	2004	15100989
genetic analysis of violacein biosynthesis by chromobacterium violaceum.	chromobacterium violaceum presents a distinctive phenotypic characteristic, the production of a deep violet pigment named violacein. although the physiological function of this pigment is not well understood, the sequencing of the genome of this bacterium has given some insight into the mechanisms and control of violacein production. it was found that erythrose-4-phosphate (e4p), a precursor to aromatic amino acid biosynthesis, is produced by the non-oxidative portion of the hexose monophosphate ...	2004	15100990
chemotaxis and flagellar genes of chromobacterium violaceum.	the availability of the complete genome of the gram-negative beta-proteobacterium chromobacterium violaceum has increasingly impacted our understanding of this microorganism. this review focuses on the genomic organization and structural analysis of the deduced proteins of the chemosensory adaptation system of c. violaceum. c. violaceum has multiple homologues of most chemotaxis genes, organized mostly in clusters in the bacterial genome. we found at least 67 genes, distributed in 10 gene cluste ...	2004	15100991
tolerance to stress and environmental adaptability of chromobacterium violaceum.	chromobacterium violaceum is a gram-negative bacterium, abundant in a variety of ecosystems in tropical and subtropical regions, including the water and borders of the negro river, a major component of the amazon basin. as a free-living microorganism, c. violaceum is exposed to a series of variable conditions, such as different sources and abundance of nutrients, changes in temperature and ph, toxic compounds and uv rays. these variations, and the wide range of environments, require great adapta ...	2004	15100992
transport genes of chromobacterium violaceum: an overview.	the complete genome sequence of the free-living bacterium chromobacterium violaceum has been determined by a consortium of laboratories in brazil. almost 500 open reading frames (orfs) coding for transport-related membrane proteins were identified in c. violaceum, which represents 11% of all genes found. the main class of transporter proteins is the primary active transporters (212 orfs), followed by electrochemical potential-driven transporters (154 orfs) and channels/pores (62 orfs). other cla ...	2004	15100993
drug resistance in chromobacterium violaceum.	chromobacterium violaceum is a free-living bacterium commonly found in aquatic habitats of tropical and subtropical regions of the world. this bacterium is able to produce a large variety of products of biotechnological and pharmacological use. although c. violaceum is considered to be non-pathogenic, some cases of severe infections in humans and other animals have been reported. genomic data on the type strain atcc 12472(t) has provided a comprehensive basis for detailed studies of pathogenicit ...	2004	15100994
chromobacterium violaceum genome: molecular mechanisms associated with pathogenicity.	chromobacterium violaceum is a versatile, gram-negative beta-protebacterium that grows in a variety of ecosystems in tropical and subtropical areas, such as the water and borders of the negro river, in the amazon region of brazil. although it is a saprophyte and is generally considered non-pathogenic, sporadic cases of human infection have been described, mainly in young children and in immunodeficient individuals. although rare, infections with c. violaceum are characterized by rapid disseminat ...	2004	15100995
energetic metabolism of chromobacterium violaceum.	chromobacterium violaceum is a free-living microorganism, normally exposed to diverse environmental conditions; it has a versatile energy-generating metabolism. this bacterium is capable of exploiting a wide range of energy resources by using appropriate oxidases and reductases. this allows c. violaceum to live in both aerobic and anaerobic conditions. in aerobic conditions, c. violaceum is able to grow in a minimal medium with simple sugars, such as glucose, fructose, galactose, and ribose; bot ...	2004	15100996
dna repair in chromobacterium violaceum.	chromobacterium violaceum is a gram-negative beta-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the negro river in the brazilian amazon. this bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. c. violaceum promotes the solubilization of gold in a mercur ...	2004	15100997
identification of chromobacterium violaceum genes with potential biotechnological application in environmental detoxification.	chromobacterium violaceum is a gram-negative bacterium found in a wide variety of tropical and subtropical ecosystems. the complete genome sequence of c. violaceum atcc 12472 is now available, and it has considerable biotechnological potential for various applications, such as environmental detoxification, as well as medical and agricultural use. we examined the biotechnological potential of c. violaceum for environmental detoxification. three operons, comprising the ars operon, involved in arse ...	2004	15100998
molecular mechanism of violacein-mediated human leukemia cell death.	violacein, a pigment isolated from chromobacterium violaceum in the amazon river, presents diverse biologic properties and attracts interest as a consequence of its antileukemic activity. elucidation of the molecular mechanism mediating this activity will provide further relevant information for understanding its effects on the cellular physiology of untransformed cells and for considering its possible clinical application. here, we show that violacein causes apoptosis in hl60 leukemic cells but ...	2004	15130948
identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin e3.	colicin e3 is a cytotoxic ribonuclease that specifically cleaves 16s rrna at the ribosomal a-site to abolish protein synthesis in sensitive escherichia coli cells. we have performed extensive mutagenesis of the 96-residue colicin e3 cytotoxic domain (e3 rrnase), assayed mutant colicins for in vivo cytotoxicity, and tested the corresponding e3 rrnase domains for their ability to inactivate ribosome function in vitro. from 21 alanine mutants, we identified five positions where mutation resulted in ...	2004	15133158
the ett2 gene cluster, encoding a second type iii secretion system from escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition.	ett2 is a second cryptic type iii secretion system in escherichia coli which was first discovered through the analysis of genome sequences of enterohemorrhagic e. coli o157:h7. comparative analyses of escherichia and shigella genome sequences revealed that the ett2 gene cluster is larger than was previously thought, encompassing homologues of genes from the spi-1, spi-2, and spi-3 salmonella pathogenicity islands. ett2-associated genes, including regulators and chaperones, were found at the same ...	2004	15150243
burkholderia cenocepacia phage bcepmu and a family of mu-like phages encoding potential pathogenesis factors.	we have isolated bcepmu, a mu-like bacteriophage whose host range includes human pathogenic burkholderia cenocepacia (formally b. cepacia genomovar iii) isolates, and determined its complete 36748 bp genomic sequence. like enteric bacteriophage mu, the bcepmu genomic dna is flanked by variable host sequences, a result of transposon-mediated replication. the bcepmu genome encodes 53 proteins, including capsid assembly components related to those of mu, and tail sheath and tube proteins related to ...	2004	15184022
biofilm development and cell death in the marine bacterium pseudoalteromonas tunicata.	the newly described green-pigmented bacterium pseudoalteromonas tunicata (d2) produces target-specific inhibitory compounds against bacteria, algae, fungi, and invertebrate larvae and is frequently found in association with living surfaces in the marine environment. as part of our studies on the ecology of p. tunicata and its interaction with marine surfaces, we examined the ability of p. tunicata to form biofilms under continuous culture conditions within the laboratory. p. tunicata biofilms ex ...	2004	15184116
use of sinorhizobium meliloti as an indicator for specific detection of long-chain n-acyl homoserine lactones.	population-density-dependent gene expression in gram-negative bacteria involves the production of signal molecules characterized as n-acyl homoserine lactones (ahls). the synthesis of ahls by numerous microorganisms has been identified by using biosensor strains based on the agrobacterium tumefaciens and chromobacterium violaceum quorum-sensing systems. the symbiotic nitrogen-fixing bacterium sinorhizobium meliloti is rapidly becoming a model organism for the study of quorum sensing. this organi ...	2004	15184178
displacements of prohead protease genes in the late operons of double-stranded-dna bacteriophages.	most of the known prohead maturation proteases in double-stranded-dna bacteriophages are shown, by computational methods, to fall into two evolutionarily independent clans of serine proteases, herpesvirus assemblin-like and clpp-like. phylogenetic analysis suggests that these two types of phage prohead protease genes displaced each other multiple times while preserving their exact location within the late operons of the phage genomes.	2004	15205439
identification of burkholderia cenocepacia genes required for bacterial survival in vivo.	burkholderia cenocepacia (formerly burkholderia cepacia complex genomovar iii) causes chronic lung infections in patients with cystic fibrosis. in this work, we used a modified signature-tagged mutagenesis (stm) strategy for the isolation of b. cenocepacia mutants that cannot survive in vivo. thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 b. cenocepacia transposon mutants, arranged in pools of ...	2004	15213146
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
effects of natural and chemically synthesized furanones on quorum sensing in chromobacterium violaceum.	cell to cell signaling systems in gram-negative bacteria rely on small diffusible molecules such as the n-acylhomoserine lactones (ahl). these compounds are involved in the production of antibiotics, exoenzymes, virulence factors and biofilm formation. they belong to the class of furanone derivatives which are frequently found in nature as pheromones, flavor compounds or secondary metabolites. to obtain more information on the relation between molecular structure and quorum sensing, we tested a ...	2004	15233843
presence of acylated homoserine lactones (ahls) and ahl-producing bacteria in meat and potential role of ahl in spoilage of meat.	quorum-sensing (qs) signals (n-acyl homoserine lactones [ahls]) were extracted and detected from five commercially produced vacuum-packed meat samples. ninety-six ahl-producing bacteria were isolated, and 92 were identified as enterobacteriaceae. hafnia alvei was the most commonly identified ahl-producing bacterium. thin-layer chromatographic profiles of supernatants from six h. alvei isolates and of extracts from spoiling meat revealed that the major ahl species had an r(f) value and shape simi ...	2004	15240313
evidence for acyl homoserine lactone signal production in bacteria associated with marine sponges.	we report for the first time the production of acyl homoserine lactones (ahls) by bacteria associated with marine sponges. given the involvement of ahls in bacterial colonization of many higher organisms, we speculate that such quorum sensing signals could play a part in interactions between sponges and the dense bacterial communities living within them.	2004	15240326
identification of a bifunctional enzyme mnmc involved in the biosynthesis of a hypermodified uridine in the wobble position of trna.	the gene encoding the bifunctional enzyme mnmc that catalyzes the two last steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2u) in trna has been previously mapped at about 50 min on the escherichia coli k12 chromosome, but to date the identity of the corresponding enzyme has not been correlated with any of the known open reading frames (orfs). using the protein fold-recognition approach, we predicted that the 74-kda product of the yfck orf located at 52.6 min and annotated as ...	2004	15247431
where does bacterial replication start? rules for predicting the oric region.	three methods, based on dna asymmetry, the distribution of dnaa boxes and dnaa gene location, were applied to identify the putative replication origins in 120 chromosomes. the chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. dna asymmetry is the most universal method of putative oric identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. the three meth ...	2004	15258248
the global regulator genes from biocontrol strain serratia plymuthica ic1270: cloning, sequencing, and functional studies.	the biocontrol activity of various fluorescent pseudomonads towards plant-pathogenic fungi is dependent upon the gaca/gacs-type two-component system of global regulators and the rpos transcription sigma factor. in particular, these components are required for the production of antifungal antibiotics and exoenzymes. to investigate the effects of these global regulators on the expression of biocontrol factors by plant-associated bacteria other than pseudomonas spp., gaca/gacs and rpos homologues w ...	2004	15262936
a simple screening protocol for the identification of quorum signal antagonists.	quorum sensing (qs) is a mechanism by which diverse microorganisms can control specific processes in response to population density. a relatively well-known form of qs among proteobacteria involves production and subsequent response to acylated homoserine lactones (ahls). quorum sensing inhibition (qsi), targeting ahl-dependent signaling, has been reported as a strategy for the control of biofilm formation used by several marine organisms. we developed a simple soft agar overlay protocol, based ...	2004	15279939
cpndb: a chaperonin sequence database.	type i chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. sequences of cpn60 genes, encoding 60-kda chaperonin protein subunits (cpn60, also known as groel or hsp60), are useful for phylogenetic studies and as targets for detection and identification of organisms. conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal pcr primers. here, we introduce cpndb, a curated collectio ...	2004	15289485
different patterns of evolution for duplicated dna repair genes in bacteria of the xanthomonadales group.	dna repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. the importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes.	2004	15333143
flow microcalorimetric studies of phenol and its chlorinated derivatives and a theoretical evaluation of their possible inhibition mode on chromobacterium violaceum respiration.	the general belief that chemical structure determines the biological effect of drugs has led to several techniques to establish structure-activity relationships (sar) that is useful in the development of more active compounds. predicting toxic effects based on sar, one can obtain toxicological data with a low cost-benefit ratio. chlorophenols that represent a class of toxic agents frequently used in industrial processes are not satisfactorily described in the literature in relation to their toxi ...	2004	15336391
in search of rnase p rna from microbial genomes.	a simple procedure has been developed to quickly retrieve and validate the dna sequence encoding the rna subunit of ribonuclease p (rnase p rna) from microbial genomes. rnase p rna sequences were identified from 94% of bacterial and archaeal complete genomes where previously no rnase p rna was annotated. a sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative rnase p rna in terms of conserved primary features an ...	2004	15337843
in vivo phosphorylation of partner switching regulators correlates with stress transmission in the environmental signaling pathway of bacillus subtilis.	exposure of bacteria to diverse growth-limiting stresses induces the synthesis of a common set of proteins which provide broad protection against future, potentially lethal stresses. among bacillus subtilis and its relatives, this general stress response is controlled by the sigmab transcription factor. signals of environmental and energy stress activate sigmab through a multicomponent network that functions via a partner switching mechanism, in which protein-protein interactions are governed by ...	2004	15342582
identification of specific in vivo-induced (ivi) genes in yersinia ruckeri and analysis of ruckerbactin, a catecholate siderophore iron acquisition system.	this work reports the utilization of an in vivo expression technology system to identify in vivo-induced (ivi) genes in yersinia ruckeri after determination of the conditions needed for its selection in fish. fourteen clones were selected, and the cloned dna fragments were analyzed after partial sequencing. in addition to sequences with no significant similarity, homology with genes encoding proteins putatively involved in two-component and type iv secretion systems, adherence, specific metaboli ...	2004	15345400
regulation of the n-acyl homoserine lactone-dependent quorum-sensing system in rhizosphere pseudomonas putida wcs358 and cross-talk with the stationary-phase rpos sigma factor and the global regulator gaca.	quorum sensing is a cell population-density dependent regulatory system which in gram-negative bacteria often involves the production and detection of n-acyl homoserine lactones (ahls). some pseudomonas putida strains have been reported to produce ahls, and one quorum-sensing locus has been identified. however, it appears that the majority of strains do not produce ahls. in this study we report the identification and regulation of the ahl-dependent system of rhizosphere p. putida wcs358. this sy ...	2004	15345437
[violacein: a molecule of biological interest originating from the soil-borne bacterium chromobacterium violaceum].	soil micro-organisms have evolved functions that allow them to withstand the strong competition for survival that characterizes most of their habitats. the production of antibiotic or antifungal compounds is one of these mechanisms. the relevant molecules often exhibit valuable therapeutic properties.	2004	15363621
complete genomic sequence of bacteriophage b3, a mu-like phage of pseudomonas aeruginosa.	bacteriophage b3 is a transposable phage of pseudomonas aeruginosa. in this report, we present the complete dna sequence and annotation of the b3 genome. dna sequence analysis revealed that the b3 genome is 38,439 bp long with a g+c content of 63.3%. the genome contains 59 proposed open reading frames (orfs) organized into at least three operons. of these orfs, the predicted proteins from 41 orfs (68%) display significant similarity to other phage or bacterial proteins. many of the predicted b3 ...	2004	15375138
metal solubilization from metal-containing solid materials by cyanogenic chromobacterium violaceum.	different cyanogenic bacterial strains (chromobacterium violaceum, pseudomonas fluorescens, bacillus megaterium) were cultivated under cyanide-forming conditions in the presence of metal-containing solids such as nickel powder or electronic scrap. all microorganisms were able to form water-soluble metal cyanides, however, with different efficiencies. c. violaceum was able to mobilize nickel as tetracyanonickelate [ni(cn)4(2-)] from fine-grained nickel powder. gold was microbially solubilized as ...	2004	15380664
pathologic quiz case: a 13-year-old boy with a 2-day history of fever, vomiting, and mental status changes. chromobacterium violaceum bacteremia.		2004	15387687
cytotoxic effects of violacein in human uveal melanoma cell lines.	violacein is the main pigment produced by chromobacterium violaceum, a saprophytic gram-negative bacillus. violacein is formed by the condensation of two modified tryptophan molecules and has potential anti-neoplastic effects. the purpose of this pilot study was to investigate the in vitro activity of violacein in human uveal melanoma cell lines. human uveal melanoma cell lines 92.1 and ocm-1 were incubated with five different concentrations of violacein (10(-5)-10(-9) m), and the total cellular ...	2004	15457100
the crystal structure of the reduced, zn2+-bound form of the b. subtilis hsp33 chaperone and its implications for the activation mechanism.	the bacterial heat shock protein hsp33 is a redox-regulated chaperone activated by oxidative stress. in response to oxidation, four cysteines within a zn2+ binding c-terminal domain form two disulfide bonds with concomitant release of the metal. this leads to the formation of the biologically active hsp33 dimer. the crystal structure of the n-terminal domain of the e. coli protein has been reported, but neither the structure of the zn2+ binding motif nor the nature of its regulatory interaction ...	2004	15458638
comparative genomics of the ftsk-hera superfamily of pumping atpases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.	recently, it has been shown that a predicted p-loop atpase (the hera or mlaa protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the trwb atpase. in this study, the ftsk-hera superfamily of p-loop atpases, in which the hera clade comprises one of the major branches, is analyzed in detail. we show that, in addition to the ftsk and hera clades, this ...	2004	15466593
an analysis of type-iii secretion gene clusters in chromobacterium violaceum.	chromobacterium violaceum is an environmental gram-negative bacterium that is common in soil and water in tropical and sub-tropical regions. it is also a model organism for studying quorum-sensing and is a rare but deadly human pathogen. recent completion of the genome sequence of c. violaceum strain atcc 12472 revealed the presence of genes associated with type-iii secretion systems (ttsss). one of these systems resembles the spi-1 system found in salmonella enterica, whereas another is similar ...	2004	15488386
the "intracellular" poly(3-hydroxybutyrate) (phb) depolymerase of rhodospirillum rubrum is a periplasm-located protein with specificity for native phb and with structural similarity to extracellular phb depolymerases.	rhodospirillum rubrum possesses a putative intracellular poly(3-hydroxybutyrate) (phb) depolymerase system consisting of a soluble phb depolymerase, a heat-stable activator, and a 3-hydroxybutyrate dimer hydrolase (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). in this study we reinvestigated the soluble r. rubrum phb depolymerase (phaz1). it turned out that phaz1 is a novel type of phb depolymerase with unique properties. purified phaz1 was specific for amorphous short-chain-len ...	2004	15489436
oxa-60, a chromosomal, inducible, and imipenem-hydrolyzing class d beta-lactamase from ralstonia pickettii.	a chromosomally encoded oxacillinase, oxa-22, had been characterized from ralstonia pickettii pic-1 that did not explain by itself the resistance profile of this strain to beta-lactams. thus, further analysis of the genetic background of this species led to the identification of another oxacillinase, oxa-60, that was expressed only after beta-lactam induction. this chromosomally encoded oxacillinase shared 19% amino acid identity with oxa-22. it has a narrow-spectrum hydrolysis profile that incl ...	2004	15504844
unique features revealed by the genome sequence of acinetobacter sp. adp1, a versatile and naturally transformation competent bacterium.	acinetobacter sp. strain adp1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized pseudomonas aeruginosa and pseudomonas putida. unlike these bacteria, the acinetobacter adp1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. the circular chromosome of the acinetobacter adp1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence ...	2004	15514110
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
regulators encoded in the escherichia coli type iii secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic e. coli o157:h7.	enterohemorrhagic escherichia coli (ehec) o157:h7 subverts host cells through a type iii secretion system encoded by the locus for enterocyte effacement (lee). genome sequencing of this pathotype revealed the existence of a gene cluster encoding components of a second cryptic type iii secretion system, e. coli type iii secretion system 2 (ett2). recently, we showed that the ett2 gene cluster is present in whole or in part in the majority of e. coli strains but is unable to encode a functional se ...	2004	15557654
genes involved in the synthesis and degradation of matrix polysaccharide in actinobacillus actinomycetemcomitans and actinobacillus pleuropneumoniae biofilms.	biofilms are composed of bacterial cells embedded in an extracellular polysaccharide matrix. a major component of the escherichia coli biofilm matrix is pga, a linear polymer of n-acetyl-d-glucosamine residues in beta(1,6) linkage. pga mediates intercellular adhesion and attachment of cells to abiotic surfaces. in this report, we present genetic and biochemical evidence that pga is also a major matrix component of biofilms produced by the human periodontopathogen actinobacillus actinomycetemcomi ...	2004	15576769
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
mitochondrial cytochrome c1 is a collapsed di-heme cytochrome.	cytochrome c(1) from mitochondrial complex iii and the di-heme cytochromes c in the corresponding enzyme from epsilon-proteobacteria have so far been considered to represent unrelated cytochromes. a missing link protein discovered in the genome of the hyperthermophilic bacterium aquifex aeolicus, however, provides evidence for a close evolutionary relationship between these two cytochromes. the mono-heme cytochrome c(1) from a. aeolicus contains stretches of strong sequence homology toward the e ...	2004	15591339
luxr homolog avhr in agrobacterium vitis affects the development of a grape-specific necrosis and a tobacco hypersensitive response.	the luxr homolog avir in agrobacterium vitis strain f2/5 was recently shown to be associated with induction of a hypersensitive response (hr) on tobacco and necrosis on grape plants, indicating that the responses are regulated by quorum sensing. we now report a second luxr homolog, avhr, whose disruption (mutant m1320) results in hr-negative and reduced grape necrosis phenotypes. the deduced avhr protein has characteristic autoinducer binding and dna binding domains and is unique among reported ...	2005	15601702
combinatorial biosynthesis of antitumor indolocarbazole compounds.	rebeccamycin and staurosporine are natural products with antitumor properties, which belong to the family of indolocarbazole alkaloids. an intense effort currently exists for the generation of indolocarbazole derivatives for the treatment of several diseases, including cancer and neurodegenerative disorders. here, we report a biological process based on combinatorial biosynthesis for the production of indolocarbazole compounds (or their precursors) in engineered microorganisms as a complementary ...	2004	15625109
combinatorial biosynthesis of antitumor indolocarbazole compounds.	rebeccamycin and staurosporine are natural products with antitumor properties, which belong to the family of indolocarbazole alkaloids. an intense effort currently exists for the generation of indolocarbazole derivatives for the treatment of several diseases, including cancer and neurodegenerative disorders. here, we report a biological process based on combinatorial biosynthesis for the production of indolocarbazole compounds (or their precursors) in engineered microorganisms as a complementary ...	2004	15625109
studies on the occurrence of gram-negative bacteria in ticks: ixodes ricinus as a potential vector of pasteurella.	a total of 372 ixodes ricinus ticks (101 females, 122 males, and 149 nymphs) collected by flagging in 6 mixed woodlands of eastern poland were examined by culture for the presence of internal gram-negative bacteria other than borrelia burgdorferi. adult ticks were examined in pools of 2 specimens each and nymphs were examined in pools of 3-5 specimens each. ticks were disinfected in 70 % ethanol and homogenized in 0.85% nacl. the diluted homogenate was inoculated onto 3 kinds of agar media: buff ...	2004	15627343
the erwinia chrysanthemi type iii secretion system is required for multicellular behavior.	enterobacterial animal pathogens exhibit aggregative multicellular behavior, which is manifested as pellicles on the culture surface and biofilms at the surface-liquid-air interface. pellicle formation behavior requires production of extracellular polysaccharide, cellulose, and protein filaments, known as curli. protein filaments analogous to curli are formed by many protein secretion systems, including the type iii secretion system (ttss). here, we demonstrate that erwinia chrysanthemi, which d ...	2005	15629935
the bldc developmental locus of streptomyces coelicolor encodes a member of a family of small dna-binding proteins related to the dna-binding domains of the merr family.	the bldc locus, required for formation of aerial hyphae in streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids d17 and d25 of a minimal ordered library. subcloning and sequencing showed that bldc encodes a member of a previously unrecognized family of small (58- to 78-residue) dna-binding proteins, related to the dna-binding domains of the merr family of transcriptional activators. bldc family members are found in a wide range of gram-positive and gram-nega ...	2005	15629942
evidence for two flagellar stators and their role in the motility of pseudomonas aeruginosa.	pseudomonas aeruginosa is a ubiquitous bacterium capable of twitching, swimming, and swarming motility. in this study, we present evidence that p. aeruginosa has two flagellar stators, conserved in all pseudomonads as well as some other gram-negative bacteria. either stator is sufficient for swimming, but both are necessary for swarming motility under most of the conditions tested, suggesting that these two stators may have different roles in these two types of motility.	2005	15629949
preliminary evaluation of the api 20ne and rapid nf plus systems for rapid identification of burkholderia pseudomallei and b. mallei.	we evaluated the api 20ne and the rapid nf plus systems with 58 burkholderia pseudomallei and 23 b. mallei strains for identification of these agents, but neither was reliable for confirmatory identification, with only 0 to 60% strains identified accurately. a greater diversity of strains in the system databases would be beneficial.	2005	15635021
antibacterial constituents from the berries of piper nigrum.	piper nigrum finds an extensive application in antibacterial preparations belonging to ayurvedic system of medicine. a bioguided extraction and fractionation of the petroleum ether extract of the berries of p. nigrum afforded 2e, 4e, 8z-n-isobutyleicosatrienamide (1), pellitorine (2), trachyone (3), pergumidiene (4) and isopiperolein b (5). pergumidiene and trachyone are isolated for the first time from p. nigrum. all the isolated compounds were active against bacillus subtilis, bacillus sphaeri ...	2004	15636188
seasonal change in bacterial flora and biomass in mountain snow from the tateyama mountains, japan, analyzed by 16s rrna gene sequencing and real-time pcr.	the bacterial flora and biomass in mountain snow from the tateyama mountains, toyama prefecture, japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal dna restriction analysis followed by 16s rrna gene sequencing and dna quantification by real-time pcr. samples of surface snow collected in various months during the melting season contained a psychrophilic bacterium, cryobacterium psychrophilum, and two psychrotrophic bacteria, variovorax paradoxus and jan ...	2005	15640179
manual and automated instrumentation for identification of enterobacteriaceae and other aerobic gram-negative bacilli.	identification of gram-negative bacilli, both enteric and nonenteric, by conventional methods is not realistic for clinical microbiology laboratories performing routine cultures in today's world. the use of commercial kits, either manual or automated, to identify these organisms is a common practice. the advent of rapid or "spot" testing has eliminated the need for some commonly isolated organisms to be identified with the systems approach. commercially available systems provide more in-depth id ...	2005	15653824
chromobacterium violaceum septicaemia from north india.	though chromobacterium violaceum is a common inhabitant of soil and water in tropical and sub-tropical regions, human infections are rare but when they do occur result in high mortality. since the first case from malaysia in 1927, about 150 cases have been reported in world literature. till date 6 cases have been reported from southern and eastern parts of india. we report here a case of c. violaceum septicaemia, probably the first case from north india. the patient, a 6 and a half year old boy ...	2004	15654137
gene cassettes potentially encoding fosfomycin resistance determinants.		2005	15673790
one-component systems dominate signal transduction in prokaryotes.	two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. by analyzing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. one-component systems are evolutionarily older, more widely distributed among bacteria and archaea, ...	2005	15680762
multiple modes of motility: a second flagellar system in escherichia coli.		2005	15687183
the flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from escherichia coli.	escherichia coli k-12 possesses two adjacent, divergent, promoterless flagellar genes, fhia-mbha, that are absent from salmonella enterica. through bioinformatics analysis, we found that these genes are remnants of an ancestral 44-gene cluster and are capable of encoding a novel flagellar system, flag-2. in enteroaggregative e. coli strain 042, there is a frameshift in lfgc that is likely to have inactivated the system in this strain. tiling path pcr studies showed that the flag-2 cluster is pre ...	2005	15687208
effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria.	soils are inhabited by many bacteria from phylogenetic groups that are poorly studied because representatives are rarely isolated in cultivation studies. part of the reason for the failure to cultivate these bacteria is the low frequency with which bacterial cells in soil form visible colonies when inoculated onto standard microbiological media, resulting in low viable counts. we investigated the effects of three factors on viable counts, assessed as numbers of cfu on solid media, and on the phy ...	2005	15691937
adaptation of the yeast ura3 selection system to gram-negative bacteria and generation of a {delta}betcde pseudomonas putida strain.	a general procedure for efficient generation of gene knockouts in gram-negative bacteria by the adaptation of the saccharomyces cerevisiae ura3 selection system is described. a pseudomonas putida strain lacking the ura3 homolog pyrf (encoding orotidine-5'-phosphate decarboxylase) was constructed, allowing the use of a plasmid-borne copy of the gene as the target of selection. the delivery vector ptec contains the pyrf gene and promoter, a conditional origin of replication (orir6k), an origin of ...	2005	15691944
effect of temperature, ph, and metals on the stability and activity of phenylalanine hydroxylase from chromobacterium violaceum.	phenylalanine hydroxylase (pah) is a non-heme iron dioxygenase catalyzing the conversion of phenylalanine to tyrosine and is present in both prokaryotic and eukaryotic organisms. a relatively simple pah is expressed by chromobacterium violaceum, a gram-negative bacterium found in tropical and subtropical regions. the effects of temperature, ph and metals on the stability and catalytic activity of chromobacterium violaceum pah were determined by steady-state kinetics, circular dichroism (cd) and ...	2005	15708798
protein domains and architectural innovation in plant-associated proteobacteria.	evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...	2005	15715905
molecular analysis of the rebeccamycin l-amino acid oxidase from lechevalieria aerocolonigenes atcc 39243.	rebeccamycin, a member of the tryptophan-derived indolocarbazole family, is produced by lechevalieria aerocolonigenes atcc 39243. the biosynthetic pathway that specifies biosynthesis of this important metabolite is comprised of 11 genes spanning 18 kb of dna. a presumed early enzyme involved in elaboration of the rebeccamycin aglycone is encoded by rebo, located at the left-hand region of the reb gene cluster. the deduced protein product, rebo (51.9 kda), is an l-amino acid oxidase (l-aao) that ...	2005	15743957
evidence for diversifying selection at the pyoverdine locus of pseudomonas aeruginosa.	pyoverdine is the primary siderophore of the gram-negative bacterium pseudomonas aeruginosa. the pyoverdine region was recently identified as the most divergent locus alignable between strains in the p. aeruginosa genome. here we report the nucleotide sequence and analysis of more than 50 kb in the pyoverdine region from nine strains of p. aeruginosa. there are three divergent sequence types in the pyoverdine region, which correspond to the three structural types of pyoverdine. the pyoverdine ou ...	2005	15743962
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
genotyping of chromobacterium violaceum isolates by reca pcr-rflp analysis.	intraspecies variation of chromobacterium violaceum was examined by comparative sequence - and by restriction fragment length polymorphism analysis of the recombinase a gene (reca-pcr-rflp). primers deduced from the known reca gene sequence of the type strain c. violaceum atcc 12472(t) allowed the specific amplification of a 1040bp reca fragment from each of the 13 c. violaceum strains investigated, whereas other closely related organisms tested negative. hindii-psti-reca rflp analysis generated ...	2005	15766789
a very rare and rapidly fatal case of chromobacterium violaceum septicemia.	chromobacterium violaceum infection is rare but causes a high mortality rate particularly in immunosuppressed persons. since its clinical presentation is non-specific and the diagnosis basically relies upon blood culture and sensitivity, this infection should be considered among the organisms targeted empirically for antibiotic therapy when a cellulitis or rapidly progressive illness follows exposure to water or soil. this is a case of fulminant septicemia caused by this rarely encountered organ ...	2004	15779589
cloning and sequencing of a genomic island found in the brazilian purpuric fever clone of haemophilus influenzae biogroup aegyptius.	a genomic island was identified in the haemophilus influenzae biogroup aegyptius brazilian purpuric fever (bpf) strain f3031. this island, which was also found in other bpf isolates, could not be detected in non-bpf biogroup aegyptius strains or in nontypeable or typeable h. influenzae strains, with the exception of a region present in the type b eagan strain. this 34,378-bp island is inserted, in reference to h. influenzae rd kw20, within a choline transport gene and contains a mosaic structure ...	2005	15784532
novel mouse model of chronic pseudomonas aeruginosa lung infection mimicking cystic fibrosis.	pseudomonas aeruginosa causes a chronic infection in the lungs of cystic fibrosis (cf) patients by establishing an alginate-containing biofilm. the infection has been studied in several animal models; however, most of the models required artificial embedding of the bacteria. we present here a new pulmonary mouse model without artificial embedding. the model is based on a stable mucoid cf sputum isolate (nh57388a) with hyperproduction of alginate due to a deletion in muca and functional n-acylhom ...	2005	15784597
ctx-m-10 linked to a phage-related element is widely disseminated among enterobacteriaceae in a spanish hospital.	ctx-m-10 has been widely disseminated among multiple clones of several species of enterobacteriaceae, harboring seemingly different plasmids, for over a decade in ramón y cajal university hospital, madrid, spain. cloning and sequencing of a 12.2-kb dna fragment from plasmid pryce21 from klebsiella pneumoniae strain kp4ac revealed a novel phage-related element immediately upstream of bla(ctx-m-10) conserved among different ctx-m-10-producing strains. this is the first report showing an extended-s ...	2005	15793141
functional insights from the distribution and role of homopeptide repeat-containing proteins.	expansion of "low complex" repeats of amino acids such as glutamine (poly-q) is associated with protein misfolding and the development of degenerative diseases such as huntington's disease. the mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (rcps) remains obscure, and the role (if any) of repeat regions remains to be determined. here, a web-accessible database of rcps is presented. the distribution and evolution of rcps t ...	2005	15805494
comprehensive characterization of the contribution of individual sigb-dependent general stress genes to stress resistance of bacillus subtilis.	the sigma(b)-dependent general stress regulon of bacillus subtilis comprises more than 150 members. induction of this regulon by imposition of environmental or metabolic stress confers multiple, nonspecific, and preemptive stress resistance to nongrowing, nonsporulated cells of b. subtilis. in this study we performed a regulon-wide phenotypic screening analysis to determine the stress sensitivity profiles of 94 mutants defective in candidate members of the general stress regulon that were previo ...	2005	15805528
6s rna is a widespread regulator of eubacterial rna polymerase that resembles an open promoter.	6s rna is an abundant noncoding rna in escherichia coli that binds to sigma70 rna polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. we have computationally identified >100 new 6s rna homologs in diverse eubacterial lineages. two abundant bacillus subtilis rnas of unknown function (bsra and bsrb) and cyanobacterial 6sa rnas are now recognized as 6s homologs. structural probing of e. coli 6s rna and a b. subtilis homolo ...	2005	15811922
azospirillum brasilense produces the auxin-like phenylacetic acid by using the key enzyme for indole-3-acetic acid biosynthesis.	an antimicrobial compound was isolated from azospirillum brasilense culture extracts by high-performance liquid chromatography and further identified by gas chromatography-mass spectrometry as the auxin-like molecule, phenylacetic acid (paa). paa synthesis was found to be mediated by the indole-3-pyruvate decarboxylase, previously identified as a key enzyme in indole-3-acetic acid (iaa) production in a. brasilense. in minimal growth medium, paa biosynthesis by a. brasilense was only observed in ...	2005	15812004
nonbioluminescent strains of photobacterium phosphoreum produce the cell-to-cell communication signal n-(3-hydroxyoctanoyl)homoserine lactone.	bioluminescence is a common phenotype in marine bacteria, such as vibrio and photobacterium species, and can be quorum regulated by n-acylated homoserine lactones (ahls). we extracted a molecule that induced a bacterial ahl monitor (agrobacterium tumefaciens nt1 [pzlr4]) from packed cod fillets, which spoil due to growth of photobacterium phosphoreum. interestingly, ahls were produced by 13 nonbioluminescent strains of p. phosphoreum isolated from the product. of 177 strains of p. phosphoreum (i ...	2005	15812045
melioidosis: epidemiology, pathophysiology, and management.	melioidosis, caused by the gram-negative saprophyte burkholderia pseudomallei, is a disease of public health importance in southeast asia and northern australia that is associated with high case-fatality rates in animals and humans. it has the potential for epidemic spread to areas where it is not endemic, and sporadic case reports elsewhere in the world suggest that as-yet-unrecognized foci of infection may exist. environmental determinants of this infection, apart from a close association with ...	2005	15831829
autoinduction in erwinia amylovora: evidence of an acyl-homoserine lactone signal in the fire blight pathogen.	erwinia amylovora causes fire blight disease of apple, pear, and other members of the rosaceae. here we present the first evidence for autoinduction in e. amylovora and a role for an n-acyl-homoserine lactone (ahl)-type signal. two major plant virulence traits, production of extracellular polysaccharides (amylovoran and levan) and tolerance to free oxygen radicals, were controlled in a bacterial-cell-density-dependent manner. two standard autoinducer biosensors, agrobacterium tumefaciens ntl4 an ...	2005	15838048
suppressive subtractive hybridization of and differences in gene expression content of calcifying and noncalcifying cultures of emiliania huxleyi strain 1516.	the marine coccolithophorid emiliania huxleyi is a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. the biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. although it has been well documented that biomineralization in e. huxleyi is prom ...	2005	15870347
identification of extracellular n-acylhomoserine lactone acylase from a streptomyces sp. and its application to quorum quenching.	n-acylhomoserine lactones (ahls) play an important role in regulating virulence factors in pathogenic bacteria. recently, the enzymatic inactivation of ahls, which can be used as antibacterial targets, has been identified in several soil bacteria. in this study, strain m664, identified as a streptomyces sp., was found to secrete an ahl-degrading enzyme into a culture medium. the ahlm gene for ahl degradation from streptomyces sp. strain m664 was cloned, expressed heterologously in streptomyces l ...	2005	15870355
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
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
identification, distribution, and expression of novel genes in 10 clinical isolates of nontypeable haemophilus influenzae.	we hypothesize that haemophilus influenzae, as a species, possesses a much greater number of genes than that found in any single h. influenzae genome. this supragenome is distributed throughout naturally occurring infectious populations, and new strains arise through autocompetence and autotransformation systems. the effect is that h. influenzae populations can readily adapt to environmental stressors. the supragenome hypothesis predicts that significant differences exist between and among the g ...	2005	15908377
quorum sensing in halophilic bacteria: detection of n-acyl-homoserine lactones in the exopolysaccharide-producing species of halomonas.	some members of the moderately halophilic genus halomonas, such as h. eurihalina, h. maura, h. ventosae and h. anticariensis, produce exopolysaccharides with applications in many industrial fields. we report here that these four species also produce autoinducer molecules that are involved in the cell-to-cell signaling process known as quorum sensing. by using the n-acyl homoserine lactone (ahl) indicator strains agrobacterium tumefaciens ntl4 (pzrl4) and chromobacterium violaceum cv026, we disco ...	2005	15909077
automatic selection of representative proteins for bacterial phylogeny.	although there are now about 200 complete bacterial genomes in genbank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence.	2005	15927057
involvement of bacterial quorum-sensing signals in spoilage of bean sprouts.	bacterial communication signals, acylated homoserine lactones (ahls), were extracted from samples of commercial bean sprouts undergoing soft-rot spoilage. bean sprouts produced in the laboratory did not undergo soft-rot spoilage and did not contain ahls or ahl-producing bacteria, although the bacterial population reached levels similar to those in the commercial sprouts, 10(8) to 10(9) cfu/g. ahl-producing bacteria (enterobacteriaceae and pseudomonads) were isolated from commercial sprouts, and ...	2005	15933035
invasive chromobacterium violaceum infection in children: case report and review.	a 3.3-year-old boy developed chromobacterium violaceum abscesses of lungs, liver and spleen and was successfully treated. he had chronic granulomatous disease (cgd). twenty-five episodes of invasive c. violaceum infection in 24 children were reviewed. all 9 cgd and 10 nonbacteremic cases survived, but 12 of 16 (75%) non-cgd and 12 of 15 (80%) bacteremic patients died.	2005	15933571
complete nucleotide sequence of the le1 prophage from the spirochete leptospira biflexa and characterization of its replication and partition functions.	the first and, to date, only extrachromosomal circular replicon identified in the spirochete leptospira is the le1 prophage from leptospira biflexa. the 74-kb le1 genome has a gc content of 36%, which is similar to the gc content of leptospira spp. most of the 79 predicted open reading frames (orfs) showed no similarities to known orfs. however 21 orfs appeared to be organized in clusters that could code for head and tail structural proteins and immunity repressor proteins. in addition, the patt ...	2005	15937155
the tetr family of transcriptional repressors.	we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ...	2005	15944459
a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts.	analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.	2005	15955239
genetic characterization of chromobacterium isolates from black water environments in the brazilian amazon.	to isolate and to characterize the diversity of chromobacterium violaceum from the brazilian amazon region.	2005	15960747
the net of life: reconstructing the microbial phylogenetic network.	it has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (hgt) events. yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. here, we present a first attempt to reconstruct such an evolutionary network, which we term the "net of life". we use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference alg ...	2005	15965028
phenylacetate catabolism in rhodococcus sp. strain rha1: a central pathway for degradation of aromatic compounds.	in gram-negative bacteria, a pathway for aerobic degradation of phenylacetic acid (paa) that proceeds via phenylacetyl-coenzyme a (coa) and hydrolytic ring fission plays a central role in the degradation of a range of aromatic compounds. in contrast, the paa pathway and its role are not well characterized in gram-positive bacteria. a cluster including 13 paa genes encoding enzymes orthologous to those of gram-negative bacteria was identified on the chromosome of rhodococcus sp. strain rha1. thes ...	2005	15968060