Publications

evaluation of the wider system, a new computer-assisted image-processing device for bacterial identification and susceptibility testing.	the wider system is a newly developed computer-assisted image-processing device for both bacterial identification and antimicrobial susceptibility testing. it has been adapted to be able to read and interpret commercial microscan panels. two hundred forty-four fresh consecutive clinical isolates (138 isolates of the family enterobacteriaceae, 25 nonfermentative gram-negative rods [nfgnrs], and 81 gram-positive cocci) were tested. in addition, 100 enterobacterial strains with known beta-lactam re ...	2000	10747104
interactions of dnaa proteins from distantly related bacteria with the replication origin of the broad host range plasmid rk2.	replication initiation of the broad host range plasmid rk2 requires binding of the host-encoded dnaa protein to specific sequences (dnaa boxes) at its replication origin (oriv). in contrast to a chromosomal replication origin, which functionally interacts only with the native dnaa protein of the organism, the ability of rk2 to replicate in a wide range of gram-negative bacterial hosts requires the interaction of oriv with many different dnaa proteins. in this study we compared the interactions o ...	2000	10749858
development of a new lysis solution for releasing genomic dna from bacterial cells for dna amplification by polymerase chain reaction.	a new lysis solution designated tz, consisting of 2.0% triton x-100 plus 2.5 mg sodium azide/ml in 0.1 m tris-hcl buffer at ph 8.0, yielded higher levels of genomic dna from escherichia coli o157:h7 cells compared with a number of other commonly used cell lysis methods. ethidium bromide stained dna bands resulting from pcr amplification of target dna from 100 cfu of e. coli o157:h7 were readily detected following electrophoresis of agarose gels. in contrast, conventional cell lysis methods faile ...	2000	10756522
a novel alliinase from onion roots. biochemical characterization and cdna cloning.	we have purified a novel alliinase (ec 4.4.1.4) from roots of onion (allium cepa l.). two isoforms with alliinase activity (i and ii) were separated by concanavalin a-sepharose and had molecular masses of 52.7 (i) and 50.5 (ii) kd on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and 51 (i) and 57.5 (ii) kd by gel filtration fast-protein liquid chromatography. isoform i had an isoelectric point of 9.3, while isoform ii had isoelectric points of 7.6, 7.9, 8.1, and 8.3. the isoforms di ...	2000	10759524
cloning and characterization of the gene encoding rna polymerase sigma factor sigma(54) of deep-sea piezophilic shewanella violacea.	we have recently reported that a sigma(54)-like factor recognizes a dna element, designated as region a, upstream of a pressure-regulated operon in piezophilic shewanella violacea strain dss12 (nakasone et al., fems microbiology lett. 176 (1999) 351-356). in this study, we isolated and characterized the rpon gene of this piezophilic bacterium. the rpon gene was found to encode a putative protein consisting of 492 amino acid residues with a predicted molecular mass of 55359 da. significant homolo ...	2000	10760597
genetic analysis of functions involved in adhesion of pseudomonas putida to seeds.	many agricultural uses of bacteria require the establishment of efficient bacterial populations in the rhizosphere, for which colonization of plant seeds often constitutes a critical first step. pseudomonas putida kt2440 is a strain that colonizes the rhizosphere of a number of agronomically important plants at high population densities. to identify the functions involved in initial seed colonization by p. putida kt2440, we subjected this strain to transposon mutagenesis and screened for mutants ...	2000	10762233
a new is4 family insertion sequence, is4bsu1, responsible for genetic instability of poly-gamma-glutamic acid production in bacillus subtilis.	certain bacillus subtilis strains, such as b. subtilis (natto) starter strains for the manufacture of natto (fermented soybeans), produce capsular poly-gamma-glutamate (gammapga). in b. subtilis (natto), gammapga synthesis is controlled by the comp-coma two-component regulatory system and thereby induced at the beginning of the stationary growth phase. we have found a new insertion sequence (is), designated is4bsu1, in the comp gene of a spontaneous gammapga-negative mutant of b. subtilis (natto ...	2000	10762236
insertion mutagenesis and membrane topology model of the pseudomonas aeruginosa outer membrane protein oprm.	pseudomonas aeruginosa oprm is a protein involved in multiple-antibiotic resistance as the outer membrane component for the mexa-mexb-oprm efflux system. planar lipid bilayer experiments showed that oprm had channel-forming activity with an average single-channel conductance of only about 80 ps in 1 m kcl. the gene encoding oprm was subjected to insertion mutagenesis by cloning of a foreign epitope from the circumsporozoite form of the malarial parasite plasmodium falciparum into 11 sites. in es ...	2000	10762238
adp-ribosylation of variants of azotobacter vinelandii dinitrogenase reductase by rhodospirillum rubrum dinitrogenase reductase adp-ribosyltransferase.	in a number of nitrogen-fixing bacteria, nitrogenase is posttranslationally regulated by reversible adp-ribosylation of dinitrogenase reductase. the structure of the dinitrogenase reductase from azotobacter vinelandii is known. in this study, mutant forms of dinitrogenase reductase from a. vinelandii that are affected in various protein activities were tested for their ability to be adp-ribosylated or to form a complex with dinitrogenase reductase adp-ribosyltransferase (drat) from rhodospirillu ...	2000	10762264
characterization of an isogenic mutant of streptococcus pyogenes manfredo lacking the ability to make streptococcal acid glycoprotein.	an isogenic mutant of streptococcus pyogenes manfredo that lacks the ability to make streptococcal acid glycoprotein (sagp) has been constructed by inserting a deletion in the sagp gene using the method of allelic exchange. an assay of cell extracts (ce) prepared from the wild-type and mutant manfredo strains for the enzyme arginine deiminase (ad) showed that significant activity was present in wild-type ce but none could be detected in mutant ce. these findings confirm our earlier conclusion th ...	2000	10768929
outer membrane protein a, peptidoglycan-associated lipoprotein, and murein lipoprotein are released by escherichia coli bacteria into serum.	complexes containing lipopolysaccharide (lps) and three outer membrane proteins (omps) are released by gram-negative bacteria incubated in human serum and into the circulation in an experimental model of sepsis. the same omps are bound by immunoglobulin g (igg) in the cross-protective antiserum raised to escherichia coli j5 (anti-j5 igg). this study was performed to identify the three omps. the 35-kda omp was identified as outer membrane protein a (ompa) by immunoblotting studies using ompa-defi ...	2000	10768945
contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from pseudomonas putida biotype b.	delta(5)-3-ketosteroid isomerase from pseudomonas putida biotype b is one of the most proficient enzymes catalyzing an allylic isomerization reaction at rates comparable to the diffusion limit. the hydrogen-bond network (asp99... wat504...tyr14...tyr55...tyr30) which links the two catalytic residues, tyr14 and asp99, to tyr30, tyr55, and a water molecule in the highly apolar active site has been characterized in an effort to identify its roles in function and stability. the deltag(u)(h2o) determ ...	2000	10769113
survival efficacy of the combination of the methioninase gene and methioninase in a lung cancer orthotopic model.	we have previously demonstrated the antitumor efficacy of recombinant methioninase (rmetase) derived from pseudomonas putida. to enhance the efficacy of rmetase, we have constructed the plgfp-metsn retrovirus encoding the p. putida methioninase (met) gene fused with the green fluorescent protein (gfp) gene. plgfp-metsn or control vector plgfpsn was introduced into the human lung cancer cell line h460. the methionine level of h460-gfp-met cells was reduced to 33% of that of h460-gfp cells. rmetas ...	2000	10770644
identification of the novobiocin biosynthetic gene cluster of streptomyces spheroides ncib 11891.	the novobiocin biosynthetic gene cluster from streptomyces spheroides ncib 11891 was cloned by using homologous deoxynucleoside diphosphate (dndp)-glucose 4,6-dehydratase gene fragments as probes. double-stranded sequencing of 25.6 kb revealed the presence of 23 putative open reading frames (orfs), including the gene for novobiocin resistance, gyrb(r), and at least 11 further orfs to which a possible role in novobiocin biosynthesis could be assigned. an insertional inactivation experiment with a ...	2000	10770754
design of a control system for biotransformation of toxic substrates: toluene hydroxylation by pseudomonas putida uv4.	using the hydroxylation of toluene to toluene cis-glycol by pseudomonas putida uv4 as an example, the design of a feed-back control system for the addition of a toxic, poorly water-soluble substrate to a fed-batch biotransformation is described. in kinetic studies the reaction followed michaelis-menten behavior until toxic toluene concentrations were reached (2.4 mm), above which irreversible denaturation of the biocatalyst was observed. an algorithm, based on a system mass balance, was used to ...	2000	10771056
characterization and expression of the pseudomonas putida bacterioferritin alpha subunit gene.	the root-colonizing pseudomonad pseudomonas putida (pp) appears to produce two subunits, alpha and beta, of the iron-binding protein, bacterioferritin. a gene encoding the alpha-bacterioferritin subunit was located adjacent to the major catalase in pp. the deduced protein sequence of the pp bfralpha gene had a very high identity with other alpha-subunits, possessing conserved amino acids responsible for ferroxidase activity. the gene also lacked a deduced methionine at residue 52, associated wit ...	2000	10773460
[microbial destruction of cyanide and thiocyanate].	the role played by a bacterial community composed of pseudomonas putida, strain 21, pseudomonas stutzeri, strain 18, and pseudomonas sp., strain 5, and by physical and chemical factors in the degradation of cn- and scn- was studied. it was shown that the degradation of cn- is determined both by the action of bacteria and by abiotic physical and chemical factors (ph, o2, temperature, the medium agitation rate, etc.). the contribution of chemical degradation was found to increase drastically at ph ...	2000	10776620
biofilm, city of microbes.		2000	10781532
deletion analysis of the escherichia coli taurine and alkanesulfonate transport systems.	the escherichia coli tauabcd and ssueadcb gene clusters are required for the utilization of taurine and alkanesulfonates as sulfur sources and are expressed only under conditions of sulfate or cysteine starvation. taud and ssud encode an alpha-ketoglutarate-dependent taurine dioxygenase and a reduced flavin mononucleotide-dependent alkanesulfonate monooxygenase, respectively. these enzymes are responsible for the desulfonation of taurine and alkanesulfonates. the amino acid sequences of ssuabc a ...	2000	10781534
haloalkane-utilizing rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism.	the sequences of the 16s rrna and haloalkane dehalogenase (dhaa) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in europe, japan, and the united states and of the archetypal haloalkane-degrading bacterium rhodococcus sp. strain ncimb13064 were compared. the 16s rrna gene sequences showed less than 1% sequence divergence, and all haloalkane degraders clearly belonged to the genus rhodococcus. all strains shared a completely conserved dhaa gene, suggesti ...	2000	10781539
the ssu locus plays a key role in organosulfur metabolism in pseudomonas putida s-313.	pseudomonas putida s-313 can utilize a broad range of aromatic sulfonates as sulfur sources for growth in sulfate-free minimal medium. the sulfonates are cleaved monooxygenolytically to yield the corresponding phenols. minitn5 mutants of strain s-313 which were no longer able to desulfurize arylsulfonates were isolated and were found to carry transposon insertions in the ssueadcbf operon, which contained genes for an atp-binding cassette-type transporter (ssuabc), a two-component reduced flavin ...	2000	10781557
fabg, an nadph-dependent 3-ketoacyl reductase of pseudomonas aeruginosa, provides precursors for medium-chain-length poly-3-hydroxyalkanoate biosynthesis in escherichia coli.	escherichia coli hosts expressing fabg of pseudomonas aeruginosa showed 3-ketoacyl coenzyme a (coa) reductase activity toward r-3-hydroxyoctanoyl-coa. furthermore, e. coli recombinants carrying the poly-3-hydroxyalkanoate (pha) polymerase-encoding gene phac in addition to fabg accumulated medium-chain-length phas (mcl-phas) from alkanoates. when e. coli fadb or fada mutants, which are deficient in steps downstream or upstream of the 3-ketoacyl-coa formation step during beta-oxidation, respective ...	2000	10781572
purification to homogeneity and characterization of a novel pseudomonas putida chromate reductase.	cr(vi) (chromate) is a widespread environmental contaminant. bacterial chromate reductases can convert soluble and toxic chromate to the insoluble and less toxic cr(iii). bioremediation can therefore be effective in removing chromate from the environment, especially if the bacterial propensity for such removal is enhanced by genetic and biochemical engineering. to clone the chromate reductase-encoding gene, we purified to homogeneity (>600-fold purification) and characterized a novel soluble chr ...	2000	10788340
quantification of phnac and nahac in contaminated new zealand soils by competitive pcr.	unculturable polycyclic aromatic hydrocarbon (pah)-degrading bacteria are a significant reservoir of the microbial potential to catabolize low-molecular-weight pahs. the population of these bacteria is larger than the population of nah-like bacteria that are the dominant organisms in culture-based studies. we used the recently described phn genes of burkholderia sp. strain rp007, which feature only rarely in culture-based studies, as an alternative genotype for naphthalene and phenanthrene degra ...	2000	10788344
isolation of adherent polycyclic aromatic hydrocarbon (pah)-degrading bacteria using pah-sorbing carriers.	two different procedures were compared to isolate polycyclic aromatic hydrocarbon (pah)-utilizing bacteria from pah-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which pahs were supplied as crystals and (ii) a new method in which pah degraders were enriched on and recovered from hydrophobic membranes containing sorbed pahs. both techniques were successful, but selected from the same source different bacterial strains able to grow on pahs a ...	2000	10788347
carbon monoxide dehydrogenase activity in bradyrhizobium japonicum.	bradyrhizobium japonicum strain 110spc4 was capable of chemolithoautotrophic growth with carbon monoxide (co) as a sole energy and carbon source under aerobic conditions. the enzyme carbon monoxide dehydrogenase (codh; ec 1.2.99.2) has been purified 21-fold, with a yield of 16% and a specific activity of 58 nmol of co oxidized/min/mg of protein, by a procedure that involved differential ultracentrifugation, anion-exchange chromatography, hydrophobic interaction chromatography, and gel filtration ...	2000	10788353
toluene monooxygenase-catalyzed epoxidation of alkenes.	several toluene monooxygenase-producing organisms were tested for their ability to oxidize linear alkenes and chloroalkenes three to eight carbons long. each of the wild-type organisms degraded all of the alkenes that were tested. epoxides were produced during the oxidation of butene, butadiene, and pentene but not hexene or octadiene. a strain of escherichia coli expressing the cloned toluene-4-monooxygenase (t4mo) of pseudomonas mendocina kr1 was able to oxidize butene, butadiene, pentene, and ...	2000	10788354
cloning and sequencing of the gene encoding an aldehyde dehydrogenase that is induced by growing alteromonas sp. strain ke10 in a low concentration of organic nutrients.	the protein composition of alteromonas sp. strain ke10 cultured at two different organic-nutrient concentrations was determined by using two-dimensional polyacrylamide gel electrophoresis. the cellular levels of three proteins, olga, -b, and -c, were considerably higher in cells grown in a low concentration of organic nutrient medium (lon medium; 0.2 mg of carbon per liter) than cells grown in a high concentration of organic nutrient medium (hon; 200 mg of c liter(-1)) or cells starved for organ ...	2000	10788355
an alpha-proteobacterium converts linear alkylbenzenesulfonate surfactants into sulfophenylcarboxylates and linear alkyldiphenyletherdisulfonate surfactants into sulfodiphenylethercarboxylates.	the surfactant linear alkylbenzenesulfonate (las; 0.5 mm) or linear monoalkyldiphenyletherdisulfonate (ladpeds; 0.5 mm) in salts medium was easily degraded in laboratory trickling filters, whereas carbon-limited, aerobic enrichment cultures in suspended culture with the same inocula did not grow. we took portions of the trickling filters which degraded ladpeds, shook the organisms from the solid support (polyester), and found that growth in suspended culture in ladpeds-salts medium occurred only ...	2000	10788359
products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria.	pyrene is a regulated pollutant at sites contaminated with polycyclic aromatic hydrocarbons (pah). it is mineralized by some bacteria but is also transformed to nonmineral products by a variety of other pah-degrading bacteria. we examined the formation of such products by four bacterial strains and identified and further characterized the most apparently significant of these metabolites. pseudomonas stutzeri strain p16 and bacillus cereus strain p21 transformed pyrene primarily to cis-4,5-dihydr ...	2000	10788360
a novel amidase (half-amidase) for half-amide hydrolysis involved in the bacterial metabolism of cyclic imides.	a novel amidase involved in bacterial cyclic imide metabolism was purified from blastobacter sp. strain a17p-4. the enzyme physiologically functions in the second step of cyclic imide degradation, i.e., the hydrolysis of monoamidated dicarboxylates (half-amides) to dicarboxylates and ammonia. enzyme production was enhanced by cyclic imides such as succinimide and glutarimide but not by amide compounds which are conventional substrates and inducers of known amidases. the purified amidase showed h ...	2000	10788365
molecular and phenotypic characterization of pseudomonas spp. isolated from milk.	putative pseudomonas spp. isolated predominantly from raw and processed milk were characterized by automated ribotyping and by biochemical reactions. isolates were biochemically profiled using the biolog system and api 20 ne and by determining the production of proteases, lipases, and lecithinases for each isolate. isolates grouped into five coherent clusters, predominated by the species p. putida (cluster a), p. fluorescens (cluster b), p. fragi (as identified by biolog) or p. fluorescens (as i ...	2000	10788386
phag-mediated synthesis of poly(3-hydroxyalkanoates) consisting of medium-chain-length constituents from nonrelated carbon sources in recombinant pseudomonas fragi.	recently, a new metabolic link between fatty acid de novo biosynthesis and biosynthesis of poly(3-hydroxy-alkanoate) consisting of medium-chain-length constituents (c(6) to c(14)) (pha(mcl)), catalyzed by the 3-hydroxydecanoyl-[acyl-carrier-protein]:coa transacylase (phag), has been identified in pseudomonas putida (b. h. a. rehm, n. krüger, and a. steinbüchel, j. biol. chem. 273:24044-24051, 1998). to establish this pha-biosynthetic pathway in a non-pha-accumulating bacterium, we functionally c ...	2000	10788390
coexistence of two different o demethylation systems in lignin metabolism by sphingomonas paucimobilis syk-6: cloning and sequencing of the lignin biphenyl-specific o-demethylase (ligx) gene.	sphingomonas paucimobilis syk-6 can grow on several dimeric model compounds of lignin as a carbon and energy source. it has o demethylation systems on three kinds of substrates: 5, 5'-dehydrodivanillic acid (ddva), syringate, and vanillate. we previously reported the cloning of a gene involved in the tetrahydrofolate-dependent o demethylation of syringate and vanillate. in the study reported here, we cloned the gene responsible for ddva o demethylation. using nitrosoguanidine mutagenesis, a muta ...	2000	10788391
construction and evaluation of a novel bifunctional n-carbamylase-d-hydantoinase fusion enzyme.	a fully enzymatic process employing two sequential enzymes, d-hydantoinase and n-carbamylase, is a typical case requiring combined enzyme activity for the production of d-amino acids. to test the possibility of generating a bifunctional fusion enzyme, we constructed a fusion protein via end-to-end fusion of a whole gene that encodes an intact protein at the n terminus of the d-hydantoinase. firstly, maltose-binding protein (mbp) gene of e. coli was fused with d-hydantoinase gene from bacillus st ...	2000	10788392
aerobic degradation of dinitrotoluenes and pathway for bacterial degradation of 2,6-dinitrotoluene.	an oxidative pathway for the mineralization of 2,4-dinitrotoluene (2, 4-dnt) by burkholderia sp. strain dnt has been reported previously. we report here the isolation of additional strains with the ability to mineralize 2,4-dnt by the same pathway and the isolation and characterization of bacterial strains that mineralize 2, 6-dinitrotoluene (2,6-dnt) by a different pathway. burkholderia cepacia strain js850 and hydrogenophaga palleronii strain js863 grew on 2,6-dnt as the sole source of carbon ...	2000	10788393
identification of fluoropyrogallols as new intermediates in biotransformation of monofluorophenols in rhodococcus opacus 1cp.	the transformation of monofluorophenols by whole cells of rhodococcus opacus 1cp was investigated, with special emphasis on the nature of hydroxylated intermediates formed. thin-layer chromatography, mass spectrum analysis, and (19)f nuclear magnetic resonance demonstrated the formation of fluorocatechol and trihydroxyfluorobenzene derivatives from each of three monofluorophenols. the (19)f chemical shifts and proton-coupled splitting patterns of the fluorine resonances of the trihydroxyfluorobe ...	2000	10788394
monitoring precursor 16s rrnas of acinetobacter spp. in activated sludge wastewater treatment systems.	recently, cangelosi and brabant used oligonucleotide probes targeting the precursor 16s rrna of escherichia coli to demonstrate that the levels of precursor rrna were more sensitive to changes in growth phase than the levels of total rrna (g. a. cangelosi and w. h. brabant, j. bacteriol. 179:4457-4463, 1997). in order to measure changes in the levels of precursor rrna in activated sludge systems, we designed oligonucleotide probes targeting the 3' region of the precursor 16s rrna of acinetobacte ...	2000	10788395
rapid identification of yersinia enterocolitica in blood by the 5' nuclease pcr assay.	yersinia enterocolitica accounts for 50% of the clinical sepsis episodes caused by the transfusion of contaminated red blood cells. a 5' nuclease taqman pcr assay was developed to detect y. enterocolitica in blood. primers and a probe based on the nucleotide sequence of the 16s rrna gene from y. enterocolitica were designed. whole-blood samples were spiked with various numbers of y. enterocolitica cells, and total chromosomal dna was extracted. when the taqman pcr assay was performed, as few as ...	2000	10790127
use of the midi-fame technique to characterize groundwater communities.	fatty acid methyl ester (fame) profiles were identified directly from groundwater microbial communities concentrated on and extracted with polycarbonate filters. the sensitivity of this direct extraction method was determined using pure cultures of acinetobacter junii, pseudomonas putida and stenotrophomonas maltophilia. a minimum concentration of 107 cells filter-1 was required to identify the predominant fatty acids from each culture. however, at least 3.7 x 109 cells filter-1 were required to ...	2000	10792531
the g-protein flhf has a role in polar flagellar placement and general stress response induction in pseudomonas putida.	the flhf gene of pseudomonas putida, which encodes a gtp-binding protein, is part of the flagellar-motility-chemotaxis operon. its disruption leads to a random flagellar arrangement in the mutant (mk107) and loss of directional motility in contrast to the wild type, which has polar flagella. the return of a normal flhf allele restores polar flagella and normal motility to mk107; its overexpression triples the flagellar number but does not restore directional motility. as flhf is homologous to th ...	2000	10792727
streptavidin-based containment systems for genetically engineered microorganisms.	the use of genetically modified microorganisms for environmental remediation continues to be debated. conditional lethal systems with tightly regulated gene expression can be used to contain released microorganisms and ameliorate some of the concerns about horizontal gene transfer. we have described streptavidin-based suicide systems to address these concerns and evaluated their function in pseudomonas putida containing the tol plasmid for aromatic hydrocarbon metabolism. tight regulation of exp ...	1999	10796996
sequence of pha synthase gene from two strains of rhodospirillum rubrum and in vivo substrate specificity of four pha synthases across two heterologous expression systems.	a 3.0-kb genomic fragment has been isolated from rhodospirillum rubrum (atcc 25903) that contains an open reading frame (orf) with strong homology to other known polyhydroxyalkanoate (pha) synthase genes. this orf has lower homology to the r. rubrum strain ha pha synthase than would be expected within the same species. we have conducted a series of heterologous expression studies evaluating the in vivo substrate specificity of pha synthase genes from rhodobacter sphaeroides, ralstonia eutropha ( ...	2000	10803898
identification of an effector specificity subregion within the aromatic-responsive regulators dmpr and xylr by dna shuffling.	the pseudomonas derived sigma(54)-dependent regulators dmpr and xylr control the expression of genes involved in catabolism of aromatic compounds. binding to distinct, nonoverlapping groups of aromatic effectors controls the activities of these transcriptional activators. previous work has derived a common mechanistic model for these two regulators in which effector binding by the n-terminal 210 residues (the a-domain) of the protein relieves repression of an intrinsic atpase activity essential ...	2000	10809676
a complex insertion sequence cluster at a point of interaction between the linear plasmid scp1 and the linear chromosome of streptomyces coelicolor a3(2).	the giant linear plasmid scp1 can integrate into the central region of the linear chromosome of streptomyces coelicolor a3(2). nucleotide sequence analysis around the target site for scp1 integration in strain m145 identified a total of five copies of four insertion sequences (iss) in a 6.5-kb dna stretch. three of the four (is468, is469, and is470) are new is elements, and the other is is466. all of these elements contain one open reading frame which encodes a transposase-like protein. two copi ...	2000	10809688
cloning and expression of ntnd, encoding a novel nad(p)(+)-independent 4-nitrobenzyl alcohol dehydrogenase from pseudomonas sp. strain tw3.	pseudomonas sp. strain tw3 is able to metabolize 4-nitrotoluene to 4-nitrobenzoate and toluene to benzoate aerobically via a route analogous to the upper pathway of the tol plasmids. we report the cloning and characterization of a benzyl alcohol dehydrogenase gene (ntnd) which encodes the enzyme for the catabolism of 4-nitrobenzyl alcohol and benzyl alcohol to 4-nitrobenzaldehyde and benzaldehyde, respectively. the gene is located downstream of the previously reported ntn gene cluster. ntnd bear ...	2000	10809692
branched-chain alpha-keto acid catabolism via the gene products of the bkd operon in enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink.	recently the bkd gene cluster from enterococcus faecalis was sequenced, and it was shown that the gene products constitute a pathway for the catabolism of branched-chain alpha-keto acids. we have now investigated the regulation and physiological role of this pathway. primer extension analysis identified the presence of a single promoter upstream of the bkd gene cluster. furthermore, a putative catabolite-responsive element was identified in the promoter region, indicative of catabolite repressio ...	2000	10809705
a bacterial sensor of plant cell contact controls the transcriptional induction of ralstonia solanacearum pathogenicity genes.	the hrp genes of the plant pathogen ralstonia solanacearum are key pathogenicity determinants; they encode a type iii protein secretion machinery involved in the secretion of mediators of the bacterium-plant interaction. these hrp genes are under the genetic control of the hrpb regulatory gene, expression of which is induced when bacteria are co-cultivated with plant cell suspensions. in this study, we used hrp-gfp transcriptional fusions to demonstrate that the expression of the hrpb and type i ...	2000	10811621
domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer aer of escherichia coli.	aerotactic responses in escherichia coli are mediated by the membrane transducer aer, a recently identified member of the superfamily of pas domain proteins, which includes sensors of light, oxygen, and redox state. initial studies of aer suggested that it might use a flavin adenine dinucleotide (fad) prosthetic group to monitor cellular redox changes. to test this idea, we purified lauryl maltoside-solubilized aer protein by his-tag affinity chromatography and showed by high performance liquid ...	2000	10811894
revised structures of the pyoverdins from pseudomonas putida cfbp 2461 and from pseudomonas fluorescens cfbp 2392.	several suggestions for structures of the siderophores (pyoverdins) from pseudomonas spp. can be found in the literature which are based on a fab mass spectrometric analysis only. availability of two original strains of two pseudomonas spp. allowed to re-investigate the structure of their pyoverdins. in both cases the amino acid sequence had to be corrected. in addition, d- and l-amino acids could be identified and located in the peptide chain. the knowledge of the correct structures is importan ...	1999	10816733
identification of sequences encoding the detoxification metalloisomerase glyoxalase i in microbial genomes from several pathogenic organisms.	the ubiquitous glyoxalase system, which is composed of two enzymes, removes cellular cytotoxic methylglyoxal (mg). in an effort to identify critical residues conserved in the evolution of the first enzyme in this system, glyoxalase i (glxi), as well as the structural implications of sequence alterations in this enzyme, a search of the national center for biotechnology information (ncbi) database of unfinished genomes was undertaken. eleven putative glxi sequences from pathogenic organisms were i ...	2000	10824093
methioninase gene therapy of human cancer cells is synergistic with recombinant methioninase treatment.	results obtained over the past 40 years have demonstrated that tumor cells of all types tested have an elevated growth requirement for methioninase compared with normal cells. recombinant methioninase (rmetase) cloned from pseudomonas putida has been found previously to be an effective antitumor agent attributable to deprivation of the extracellular methionine source of the tumor. to degrade intracellular methioninase, we have now developed an adenoviral vector inserted with the p. putida methio ...	2000	10825143
pseudomonas plecoglossicida sp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, plecoglossus altivelis.	a new pseudomonas species, for which the name pseudomonas plecoglossicida is proposed, was isolated from cultured ayu (plecoglossus altivelis) with bacterial haemorrhagic ascites. the causative agent was similar to pseudomonas putida biovar a in its phenotypic characteristics and on the basis of 16s rrna gene sequence analysis, but it reduced nitrate to nitrite. furthermore, it was distinguished phenotypically from pseudomonas putida biovar a by utilization of d-malate, l-(+)-tartrate, m-tartrat ...	2000	10826790
engineering outer-membrane proteins in pseudomonas putida for enhanced heavy-metal bioadsorption.	metallothioneins (mts) are small, cysteine-rich proteins with a strong metal-binding capacity that are ubiquitous in the animal kingdom. recombinant expression of mt fused to outer-membrane components of gram-negative bacteria may provide new methods to treat heavy-metal pollution in industrial sewage. in this work, we have engineered pseudomonas putida, a per se highly robust microorganism able to grow in highly contaminated habitats in order to further increase its metal-chelating ability. we ...	2000	10830869
distribution of aldoxime dehydratase in microorganisms.	the distribution of phenylacetaldoxime-degrading and pyridine-3-aldoxime-degrading ability was examined with intact cells of 975 microorganisms, including 45 genera of bacteria, 11 genera of actinomyces, 22 genera of yeasts, and 37 genera of fungi, by monitoring the decrease of the aldoximes by high-pressure liquid chromatography. the abilities were found to be widely distributed in bacteria, actinomyces, fungi, and some yeasts: 98 and 107 strains degraded phenylacetaldoxime and pyridine-3-aldox ...	2000	10831401
bioconversion of ferulic acid into vanillic acid by means of a vanillate-negative mutant of pseudomonas fluorescens strain bf13.	from a ferulic-acid-degrading pseudomonas fluorescens strain (bf13), we have isolated a transposon mutant, which retained the ability to bioconvert ferulic acid into vanillic acid but lost the ability to further degrade the latter acid. the mutant, bf13-97, was very stable, and therefore it was suitable to be used as a biocatalyst for the preparative synthesis of vanillic acid from ferulic acid. by use of resting cells we determined the effect on the bioconversion rate of several parameters, suc ...	2000	10831404
biotransformation of hydroxylaminobenzene and aminophenol by pseudomonas putida 2np8 cells grown in the presence of 3-nitrophenol.	biotransformation products of hydroxylaminobenzene and aminophenol produced by 3-nitrophenol-grown cells of pseudomonas putida 2np8, a strain grown on 2- and 3-nitrophenol, were characterized. ammonia, 2-aminophenol, 4-aminophenol, 4-benzoquinone, n-acetyl-4-aminophenol, n-acetyl-2-aminophenol, 2-aminophenoxazine-3-one, 4-hydroquinone, and catechol were produced from hydroxylaminobenzene. ammonia, n-acetyl-2-aminophenol, and 2-aminophenoxazine-3-one were produced from 2-aminophenol. all of these ...	2000	10831408
osmoprotection by pipecolic acid in sinorhizobium meliloti: specific effects of d and l isomers.	dl-pipecolic acid (dl-pip) promotes growth restoration of sinorhizobium meliloti cells facing inhibitory hyperosmolarity. surprisingly, d and l isomers of this imino acid supplied separately were not effective. the uptake of l-pip was significantly favored in the presence of the d isomer and by a hyperosmotic stress. chromatographic analysis of the intracellular solutes showed that stressed cells did not accumulate radiolabeled l-pip. rather, it participates in the synthesis of the main endogeno ...	2000	10831411
prey range characterization, ribotyping, and diversity of soil and rhizosphere bdellovibrio spp. isolated on phytopathogenic bacteria.	thirty new bdellovibrio strains were isolated from an agricultural soil and from the rhizosphere of plants grown in that soil. using a combined molecular and culture-based approach, we found that the soil bdellovibrios included subpopulations of organisms that differed from rhizosphere bdellovibrios. thirteen soil and seven common bean rhizosphere bdellovibrio strains were isolated when pseudomonas corrugata was used as prey; seven and two soil strains were isolated when erwinia carotovora subsp ...	2000	10831412
bacterial community structure and physiological state within an industrial phenol bioremediation system.	the structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. rapid community fingerprinting by pcr-based denaturing gradient gel electrophoresis (dgge) of 16s rdna indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclu ...	2000	10831417
differential effects of permeating and nonpermeating solutes on the fatty acid composition of pseudomonas putida.	we examined the effect of reduced water availability on the fatty acid composition of pseudomonas putida strain mt-2 grown in a defined medium in which the water potential was lowered with the permeating solutes nacl or polyethylene glycol (peg) with a molecular weight of 200 (peg 200) or the nonpermeating solute peg 8000. transmission electron microscopy showed that -1.0-mpa peg 8000-treated cells had convoluted outer membranes, whereas -1.0-mpa nacl-treated or control cells did not. at the ran ...	2000	10831419
use of randomly amplified polymorphic dna as a means of developing genus- and strain-specific streptomyces dna probes.	we have analyzed 20 randomly amplified polymorphic dna (rapd) primers against 36 streptomyces strains, including 17 taxonomically undefined strains, 25 nonstreptomycete actinomycetes, and 12 outgroups consisting of gram-positive and -negative species. most of the primers were useful in identifying unique dna polymorphisms of all strains tested. we have used rapd techniques to develop a genus-specific probe, one not necessarily targeting the ribosomal gene, for streptomyces, and a strain-specific ...	2000	10831438
methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates.	miniaturized growth systems for heterogeneous culture collections are not only attractive in reducing demands for incubation space and medium but also in making the parallel handling of large numbers of strains more practicable. we report here on the optimization of oxygen transfer rates in deep-well microtiter plates and the development of a replication system allowing the simultaneous and reproducible sampling of 96 frozen glycerol stock cultures while the remaining culture volume remains froz ...	2000	10831450
detection of pseudomonas savastanoi pv. savastanoi in olive plants by enrichment and pcr.	the sequence of the gene iaal of pseudomonas savastanoi ew2009 was used to design primers for pcr amplification. the iaal-derived primers directed the amplification of a 454-bp fragment from genomic dna isolated from 70 strains of p. savastanoi, whereas genomic dna from 93 non-p. savastanoi isolates did not yield this amplified product. a previous bacterial enrichment in the semiselective liquid medium pvf-1 improved the pcr sensitivity level, allowing detection of 10 to 100 cfu/ml of plant extr ...	2000	10831456
heterologous expression in pseudomonas aeruginosa and purification of the 9.2-kda c-type cytochrome subunit of p-cresol methylhydroxylase.	the 9.2-kda c-type cytochrome subunit (pchc) of the flavocytochrome p-cresol methylhydroxylase from pseudomonas putida ncimb 9869 has been overexpressed in recombinant form in pseudomonas aeruginosa pao1-lac, using the recently developed pucp-nde vector. efforts to produce the cytochrome in escherichia coli using a pet vector, with or without its signal peptide, were generally unsuccessful, yielding relatively low levels of the protein. in contrast, the mature form of pchc accumulated in the per ...	2000	10833393
influence of the histidine tail on the structure and activity of recombinant chlorocatechol 1,2-dioxygenase.	we present two efficient expression systems for the chlorocatechol 1, 2-dioxygenase (ccd) from pseudomonas putida. in the first, ccd (encoded by the clca gene) was expressed in the petclca vector with the addition of an n-terminal histidine tail. after purification, the enzyme (ccd 6xhis) was proteolytically cleaved with thrombin to remove the his tail. the cd spectra of the cleaved and uncleaved enzymes present only minor differences, indicative of correct protein folding. however, the activity ...	2000	10833439
benzoylformate decarboxylase from pseudomonas putida as stable catalyst for the synthesis of chiral 2-hydroxy ketones.	the thiamin diphosphate- and mg2+-dependent enzyme benzoylformate decarboxylase (bfd) from pseudomonas putida was characterized with respect to its suitability to catalyze the formation of chiral 2-hydroxy ketones in a benzoin-condensation type reaction. carboligation constitutes a side reaction of bfd, whereas the predominant physiological task of the enzyme is the non-oxidative decarboxylation of benzoylformate. for this purpose the enzyme was obtained in sufficient purity from pseudomonas put ...	2000	10840971
catalytic role of enzymes: short strong h-bond-induced partial proton shuttles and charge redistributions.	a two-step reaction mechanism (catalyzed alternatively by acid and base) with partial proton shuttles and charge redistributions promoted by short strong h bonds (sshbs) (playing a dual role as an amphi-acid/base catalyst) is proposed to explain the enormous rate enhancement observed in enzymatic reactions involving carbanion intermediates. the sshbs in the two-step reactions are found to be responsible for enhancing enzyme-substrate interactions in favor of the transition state structure over t ...	2000	10841545
pas domain residues involved in signal transduction by the aer redox sensor of escherichia coli.	pas domains sense oxygen, redox potential and light, and are implicated in behaviour, circadian rhythmicity, development and metabolic regulation. although pas domains are widespread in archaea, bacteria and eukaryota, the mechanism of signal transduction has been elucidated only for the bacterial photo sensor pyp and oxygen sensor fixl. we investigated the signalling mechanism in the pas domain of aer, the redox potential sensor and aerotaxis transducer in escherichia coli. forty-two residues i ...	2000	10844669
evolution of a degradative bacterial consortium during the enrichment of naphtha solvent.	a microbial mixed culture able to degrade naphtha solvent, a model of hydrocarbon aromatic mixture, was isolated from a hydrocarbon-polluted soil. composition of the population was monitored by phenotypic and molecular methods applied on soil dna, on whole enrichment culture dna, and on 85 isolated strains. strains were characterized for their 16s rdna restriction profiles and for their random amplified polymorphic dna profiles. catabolic capabilities were monitored by phenotypic traits and by p ...	2000	10849177
a novel magnetite-immobilized cell process for heavy metal removal from industrial effluent.	the sorption and desorption of copper (ii) (cu[ii]) ions from the wastewater by magnetite-immobilized cells of pseudomonas putida 5-x with acidic pretreatment were studied. pretreating cells with 0.6 n hcl was found to enhance greatly the adsorption capacity of biomass up to 85.6 mg/g and had no significant effect on the loss of p. putida 5-x cells during biosorbent pretreatment. the biosorption capacity to cu2+ of magnetite-immobilized cells of p. putida 5-x harvested during various growth phas ...	2000	10849862
purification and characterization of sa-lrp, a dna-binding protein from the extreme thermoacidophilic archaeon sulfolobus acidocaldarius homologous to the bacterial global transcriptional regulator lrp.	archaea, constituting the third primary domain of life, harbor a basal transcription apparatus of the eukaryotic type, whereas curiously, a large fraction of the potential transcription regulation factors appear to be of the bacterial type. to date, little information is available on these predicted regulators and on the intriguing interplay that necessarily has to occur with the transcription machinery. here, we focus on sa-lrp of the extremely thermoacidophilic crenarchaeote sulfolobus acidoca ...	2000	10850980
comp, a pilin-like protein essential for natural competence in acinetobacter sp. strain bd413: regulation, modification, and cellular localization.	we recently identified a pilin-like competence factor, comp, which is essential for natural transformation of the gram-negative soil bacterium acinetobacter sp. strain bd413. here we demonstrate that transcription and synthesis of the pilin-like competence factor comp are maximal in the late stationary growth phase, whereas competence is induced immediately after inoculation of a stationary-phase culture into fresh medium. western blot analyses revealed three forms of comp, one with an apparent ...	2000	10850981
analysis of the polar flagellar gene system of vibrio parahaemolyticus.	vibrio parahaemolyticus has dual flagellar systems adapted for locomotion under different circumstances. a single, sheathed polar flagellum propels the swimmer cell in liquid environments. numerous unsheathed lateral flagella move the swarmer cell over surfaces. the polar flagellum is produced continuously, whereas the synthesis of lateral flagella is induced under conditions that impede the function of the polar flagellum, e.g., in viscous environments or on surfaces. thus, the organism possess ...	2000	10850984
genetic investigation of the catabolic pathway for degradation of abietane diterpenoids by pseudomonas abietaniphila bkme-9.	we have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by pseudomonas abietaniphila bkme-9. the dit gene cluster is located on a 16.7-kb dna fragment containing 13 complete open reading frames (orfs) and 1 partial orf. the genes dita1a2a3 encode the alpha and beta subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. the dioxygenase mutant ...	2000	10850995
physical morphology and surface properties of unsaturated pseudomonas putida biofilms.	unsaturated biofilms of pseudomonas putida, i.e., biofilms grown in humid air, were analyzed by atomic force microscopy to determine surface morphology, roughness, and adhesion forces in the outer and basal cell layers of fresh and desiccated biofilms. desiccated biofilms were equilibrated with a 75.5% relative humidity atmosphere, which is far below the relative humidity of 98 to 99% at which these biofilms were cultured. in sharp contrast to the effects of drying on biofilms grown in fluid, we ...	2000	10850998
inactivation of gltb abolishes expression of the assimilatory nitrate reductase gene (nasb) in pseudomonas putida kt2442.	by using mini-tn5 transposon mutagenesis, random transcriptional fusions of promoterless bacterial luciferase, luxab, to genes of pseudomonas putida kt2442 were generated. insertion mutants that responded to ammonium deficiency by induction of bioluminescence were selected. the mutant that responded most strongly was genetically analyzed and is demonstrated to bear the transposon within the assimilatory nitrate reductase gene (nasb) of p. putida kt2442. genetic evidence as well as sequence analy ...	2000	10852866
salmonella enterica serovar typhimurium peptidase b is a leucyl aminopeptidase with specificity for acidic amino acids.	peptidase b (pepb) of salmonella enterica serovar typhimurium is one of three broad-specificity aminopeptidases found in this organism. we have sequenced the pepb gene and found that it encodes a 427-amino-acid (46.36-kda) protein, which can be unambiguously assigned to the leucyl aminopeptidase (lap) structural family. pepb has been overexpressed and purified. the active enzyme shows many similarities to other members of the lap family: it is a heat-stable (70 degrees c; 20 min) hexameric ( app ...	2000	10852868
virulence of the phytopathogen pseudomonas syringae pv. maculicola is rpon dependent.	we cloned the rpon (ntra and glnf) gene encoding sigma(54) from the phytopathogen pseudomonas syringae pv. maculicola strain es4326. the p. syringae es4326 rpon gene complemented pseudomonas aeruginosa, escherichia coli, and klebsiella aerogenes rpon mutants for a variety of rpon mutant phenotypes, including the inability to utilize nitrate as sole nitrogen source. dna sequence analysis of the p. syringae es4326 rpon gene revealed that the deduced amino acid sequence was most similar (86% identi ...	2000	10852883
the alternative sigma factor rpon is required for hrp activity in pseudomonas syringae pv. maculicola and acts at the level of hrpl transcription.	beta-glucuronidase (uida) reporter gene fusions were constructed for the hrpz, hrpl, and hrps genes from the phytopathogen pseudomonas syringae pv. maculicola strain es4326. these reporters, as well as an avrrpt2-uida fusion, were used to measure transcriptional activity in es4326 and a es4326 rpon mutant. rpon was required for the expression of avrrpt2, hrpz, and hrpl in vitro in minimal media and in vivo when infiltrated into arabidopsis thaliana leaves. in contrast, the expression of hrps was ...	2000	10852884
isolation and characterization of nonchemotactic chez mutants of escherichia coli.	the escherichia coli chez protein stimulates dephosphorylation of chey, a response regulator in the chemotaxis signal transduction pathway, by an unknown mechanism. genetic analysis of chez has lagged behind biochemical and biophysical characterization. to identify putative regions of functional importance in chez, we subjected chez to random mutagenesis and isolated 107 nonchemotactic chez mutants. missense mutations clustered in six regions of chez, whereas nonsense and frameshift mutations we ...	2000	10852888
chlorocatechol detection based on a clc operon/reporter gene system.	a sensitive and selective sensing system for chlorocatechols (3-chlorocatechol and 4-chlorocatechol) was developed based on pseudomonas putida bacteria harboring the plasmid psmm50r-b'. in this plasmid, the regulatory protein of the clc operon, clcr, controls the expression of the reporter enzyme beta-galactosidase. when bacteria containing components of the clc operon are grown in the presence of chlorocatechols, clcr activates the clca promoter, which is located upstream from the beta-galactos ...	2000	10857616
high intracellular level of guanosine tetraphosphate in mycobacterium smegmatis changes the morphology of the bacterium.	almost one-third of the world population today harbors the tubercle bacillus asymptomatically. it is postulated that the morphology and staining pattern of the long-term persistors are different from those of actively growing culture. interestingly, it has been found that the morphology and staining pattern of the starved in vitro population of mycobacteria is similar to the persistors obtained from the lung lesions. in order to delineate the biochemical characteristics of starved mycobacteria, ...	2000	10858225
kinetic analysis of a tod-lux bacterial reporter for toluene degradation and trichloroethylene cometabolism.	kinetics of toluene and trichloroethylene (tce) degradation and bioluminescence from the bioreporter pseudomonas putida b2 and tva8 were investigated utilizing batch and continuous culture, respectively. degradation was modeled using a michaelis-menten expression for the competition of two substrates for a single enzyme system, and bioluminescence was modeled assuming a luciferase enzyme saturational dependence on toluene as the inducer and growth substrate. during the batch experiments, biolumi ...	2000	10861405
isothiocyanates in myrosinase treated herb extract of cleome chrysantha decne. and their antimicrobial activities.	gc/ms analysis of the volatiles produced by the action of endogenous myrosinase in cleome chrysantha decne. herb, showed three major components, 1-isocyano-4-methyl benzene, gamma-muurolene and (cis) nerolidole (21.72%, 12.15% and 10.39%, respectively). 1-isocyano-4-methyl benzene is not produced from myrosinase treated seeds of cleome chrysantha decne., while muurolene and nerolidole were found at higher concentrations 16.1% and 13.67%, respectively. some other isothiocyanates identified in the ...	2000	10861975
biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for pseudomonas putida f1.	although microbial growth on substrate mixtures is commonly encountered in bioremediation, wastewater treatment, and fermentation, mathematical modeling of mixed substrate kinetics has been limited. we report the kinetics of pseudomonas putida f1 growing on benzene, toluene, phenol, and their mixtures, and compare mathematical models to describe these results. the three aromatics are each able to act as carbon and energy sources for this strain. biodegradation rates were measured in batch cultiv ...	2000	10862677
a regulatory rna (prrb rna) modulates expression of secondary metabolite genes in pseudomonas fluorescens f113.	the gacs-gaca two-component signal transduction system, which is highly conserved in gram-negative bacteria, is required for the production of exoenzymes and secondary metabolites in pseudomonas spp. screening of a pseudomonas fluorescens f113 gene bank led to the isolation of a previously undefined locus which could restore secondary metabolite production to both gacs and gaca mutants of f113. sequence analysis of this locus demonstrated that it did not contain any obvious pseudomonas protein-c ...	2000	10869066
the pseudomonas aeruginosa devb/sol homolog, pgl, is a member of the hex regulon and encodes 6-phosphogluconolactonase.	a cyclic version of the entner-doudoroff pathway is used by pseudomonas aeruginosa to metabolize carbohydrates. genes encoding the enzymes that catabolize intracellular glucose to pyruvate and glyceraldehyde 3-phosphate are coordinately regulated, clustered at 39 min on the chromosome, and collectively form the hex regulon. within the hex cluster is an open reading frame (orf) with homology to the devb/sol family of unidentified proteins. this orf encodes a protein of either 243 or 238 amino aci ...	2000	10869070
influence of deletions within domain ii of exotoxin a on its extracellular secretion from pseudomonas aeruginosa.	pseudomonas aeruginosa is a gram-negative bacterium that secretes many proteins into the extracellular medium via the xcp machinery. this pathway, conserved in gram-negative bacteria, is called the type ii pathway. the exoproteins contain information in their amino acid sequence to allow targeting to their secretion machinery. this information may be present within a conformational motif. the nature of this signal has been examined for p. aeruginosa exotoxin a (pe). previous studies failed to id ...	2000	10869085
expansion of the clavulanic acid gene cluster: identification and in vivo functional analysis of three new genes required for biosynthesis of clavulanic acid by streptomyces clavuligerus.	clavulanic acid is a potent inhibitor of beta-lactamase enzymes and is of demonstrated value in the treatment of infections by beta-lactam-resistant bacteria. previously, it was thought that eight contiguous genes within the genome of the producing strain streptomyces clavuligerus were sufficient for clavulanic acid biosynthesis, because they allowed production of the antibiotic in a heterologous host (k. a. aidoo, a. s. paradkar, d. c. alexander, and s. e. jensen, p. 219-236, in v. p. gullo et ...	2000	10869089
effect of model sorptive phases on phenanthrene biodegradation: different enrichment conditions influence bioavailability and selection of phenanthrene-degrading isolates.	the sorption of organic contaminants by natural organic matter (nom) often limits substrate bioavailability and is an important factor affecting microbial degradation rates in soils and sediments. we hypothesized that reduced substrate bioavailability might influence which microbial assemblages are responsible for contaminant degradation under enrichment culture conditions. our primary goal was to characterize enrichments in which different model organic solid phases were used to establish a ran ...	2000	10877757
genes expressed in pseudomonas putida during colonization of a plant-pathogenic fungus.	in vivo expression technology (ivet) was employed to study colonization of phytophthora parasitica by a biological control bacterium, pseudomonas putida 06909, based on a new selection marker. the pyrb gene, which encodes aspartate transcarbamoylase, an enzyme used for pyrimidine biosynthesis, was cloned from p. putida 06909. a pyrb-disrupted mutant did not grow in pyrimidine-deficient media unless it was complemented with pyrbc' behind an active promoter. thirty clones obtained from p. putida 0 ...	2000	10877766
biocontrol of the sugarcane borer eldana saccharina by expression of the bacillus thuringiensis cry1ac7 and serratia marcescens chia genes in sugarcane-associated bacteria.	the cry1ac7 gene of bacillus thuringiensis strain 234, showing activity against the sugarcane borer eldana saccharina, was cloned under the control of the tac promoter. the fusion was introduced into the broad-host-range plasmid pkt240 and the integration vector pjff350 and without the tac promoter into the broad-host-range plasmids pml122 and pkmm0. these plasmids were introduced into a pseudomonas fluorescens strain isolated from the phylloplane of sugarcane and the endophytic bacterium herbas ...	2000	10877771
molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in pseudomonas strains isolated from different contaminated sites in belarus.	twenty different pseudomonas strains utilizing m-toluate were isolated from oil-contaminated soil samples near minsk, belarus. seventeen of these isolates carried plasmids ranging in size from 78 to about 200 kb (assigned psvs plasmids) and encoding the meta cleavage pathway for toluene metabolism. most plasmids were conjugative but of unknown incompatibility groups, except for one, which belonged to the incp9 group. the organization of the genes for toluene catabolism was determined by restrict ...	2000	10877777
isolation and characterization of 2,3-dichloro-1-propanol-degrading rhizobia.	2,3-dichloro-1-propanol is more chemically stable than its isomer, 1, 3-dichloro-2-propanol, and is therefore more difficult to degrade. the isolation of bacteria capable of complete mineralization of 2, 3-dichloro-1-propanol was successful only from enrichments at high ph. the bacteria thus isolated were found to be members of the alpha division of the proteobacteria in the rhizobium subdivision, most likely agrobacterium sp. they could utilize both dihaloalcohol substrates and 2-chloropropioni ...	2000	10877782
bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading comamonas testosteroni strain, i2gfp.	a strain identified as comamonas testosteroni i2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-ca). during the mineralization, a yellow intermediate accumulated temporarily, due to the distal meta-cleavage of chlorocatechol. this strain was tested for its ability to clean wastewater containing 3-ca upon inoculation into activated sludge. to monitor its survival, the strain was chromosomally marked with the gfp gene and designated i2gfp. after inoculatio ...	2000	10877785
influence of chlorine substituents on rates of oxidation of chlorinated biphenyls by the biphenyl dioxygenase of burkholderia sp. strain lb400.	biphenyl dioxygenase from burkholderia (pseudomonas) sp. strain lb400 catalyzes the first reaction of a pathway for the degradation of biphenyl and a broad range of chlorinated biphenyls (cbs). the effect of chlorine substituents on catalysis was determined by measuring the specific activity of the enzyme with biphenyl and 18 congeners. the catalytic oxygenase component was purified and incubated with individual cbs in the presence of electron transport proteins and cofactors that were required ...	2000	10877788
molecular analysis of surfactant-driven microbial population shifts in hydrocarbon-contaminated soil.	we analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. a mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. witconol sn70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (cmc) in soil (cmc') (determined to be 13 mg g(-1)). addition of the surfactant at a concentration below the cmc' (2 ...	2000	10877792
sequence analysis and initial characterization of two isozymes of hydroxylaminobenzene mutase from pseudomonas pseudoalcaligenes js45.	pseudomonas pseudoalcaligenes js45 grows on nitrobenzene by a partially reductive pathway in which the intermediate hydroxylaminobenzene is enzymatically rearranged to 2-aminophenol by hydroxylaminobenzene mutase (hab mutase). the properties of the enzyme, the reaction mechanism, and the evolutionary origin of the gene(s) encoding the enzyme are unknown. in this study, two open reading frames (haba and habb), each encoding an hab mutase enzyme, were cloned from a p. pseudoalcaligenes js45 genomi ...	2000	10877793
cloning of the malic enzyme gene from corynebacterium glutamicum and role of the enzyme in lactate metabolism.	malic enzyme is one of at least five enzymes, known to be present in corynebacterium glutamicum, capable of carboxylation and decarboxylation reactions coupling glycolysis and the tricarboxylic acid cycle. to date, no information is available concerning the physiological role of the malic enzyme in this bacterium. the male gene from c. glutamicum has been cloned and sequenced. the protein encoded by this gene has been purified to homogeneity, and the biochemical properties have been established. ...	2000	10877795