Publications

allylic or benzylic stabilization is essential for catalysis by bacterial benzyl alcohol dehydrogenases.	benzyl alcohol dehydrogenase from acinetobacter calcoaceticus (ac-badh) and tol plasmid-encoded benzyl alcohol dehydrogenase from pseudomonas putida (tol-badh) have previously been shown to oxidize a variety of aromatic alcohols but not aliphatic substrates. here, we have expressed the genes for ac-badh and tol-badh in escherichia coli, purified the resulting over-expressed enzymes, and shown that each is an effective catalyst of both benzylic and allylic alcohol oxidation, but not of oxidation ...	1999	10334943
the iiantr (ptsn) protein of pseudomonas putida mediates the c source inhibition of the sigma54-dependent pu promoter of the tol plasmid.	the gene cluster adjacent to the sequence of rpon (encoding sigma factor sigma54) of pseudomonas putida has been studied with respect to the c source regulation of the pu promoter of the upper tol (toluene catabolism) operon. the region includes four open reading frames (orfs), two of which (named ptsn and ptso genes) encode proteins similar to components of the phosphoenolpyruvate:sugar phosphotransferase system. each of the four genes was disrupted with a nonpolar insertion, and the effects in ...	1999	10336451
genetic characterization of wild-type and mutant fur genes of bordetella avium.	for most, if not all, organisms, iron (fe) is an essential element. in response to the nutritional requirement for fe, bacteria evolved complex systems to acquire the element from the environment. the genes encoding these systems are often coordinately regulated in response to the fe concentration. recent investigations revealed that bordetella avium, a respiratory pathogen of birds, expressed a number of fe-regulated genes (t. d. connell, a. dickenson, a. j. martone, k. t. militello, m. j. fili ...	1999	10338537
cloning and characterization of mdc genes encoding malonate decarboxylase from pseudomonas putida.	the dna fragment encoding malonate decarboxylase, involved in malonate assimilation, was cloned from pseudomonas putida. the 11-kb dna fragment contained nine open reading frames, which were designated mdcabcdeghlm in the given order. n-terminal protein sequencing established that the mdca, mdcc, mdcd, mdce and mdch genes encoded subunits alpha, delta, beta, gamma and epsilon of the malonate decarboxylase, respectively. malonate decarboxylase was functionally expressed in escherichia coli from p ...	1999	10339824
chemoselective nitro group reduction and reductive dechlorination initiate degradation of 2-chloro-5-nitrophenol by ralstonia eutropha jmp134.	ralstonia eutropha jmp134 utilizes 2-chloro-5-nitrophenol as a sole source of nitrogen, carbon, and energy. the initial steps for degradation of 2-chloro-5-nitrophenol are analogous to those of 3-nitrophenol degradation in r. eutropha jmp134. 2-chloro-5-nitrophenol is initially reduced to 2-chloro-5-hydroxylaminophenol, which is subject to an enzymatic bamberger rearrangement yielding 2-amino-5-chlorohydroquinone. the chlorine of 2-amino-5-chlorohydroquinone is removed by a reductive mechanism, ...	1999	10347008
an alkane-responsive expression system for the production of fine chemicals	membrane-located monooxygenase systems, such as the pseudomonas putida mt-2-derived xylene oxygenase, are attractive for challenging transformations of apolar compounds, including enantiospecific epoxidations, but are difficult to synthesize at levels that are useful for application to biotechnological processes. in order to construct efficient biocatalysis strains, we utilized the alkane-responsive regulatory system of the oct plasmid-located alk genes of pseudomonas oleovorans gpo1, a very att ...	1999	10347009
monooxygenase-mediated 1,2-dichloroethane degradation by pseudomonas sp. strain dca1.	a bacterial strain, designated pseudomonas sp. strain dca1, was isolated from a 1,2-dichloroethane (dca)-degrading biofilm. strain dca1 utilizes dca as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. the affinity of strain dca1 for dca is very high, with a km value below the detection limit of 0.5 microm. instead of a hydrolytic dehalogenation, as in other dca utilizers, the first step in dca degradation in strain dca1 is ...	1999	10347028
role of pfka and general carbohydrate catabolism in seed colonization by enterobacter cloacae.	enterobacter cloacae a-11 is a transposon mutant of strain 501r3 that was deficient in cucumber spermosphere colonization and in the utilization of certain carbohydrates (d. p. roberts, c. j. sheets, and j. s. hartung, can. j. microbiol. 38:1128-1134, 1992). in vitro growth of strain a-11 was reduced or deficient on most carbohydrates that supported growth of strain 501r3 but was unaffected on fructose, glycerol, and all amino acids and organic acids tested. colonization by strain a-11 was signi ...	1999	10347036
characterization of a pseudomonas putida allylic alcohol dehydrogenase induced by growth on 2-methyl-3-buten-2-ol.	we have been working to develop an enzymatic assay for the alcohol 2-methyl-3-buten-2-ol (232-mb), which is produced and emitted by certain pines. to this end we have isolated the soil bacterium pseudomonas putida mb-1, which uses 232-mb as a sole carbon source. strain mb-1 contains inducible 3-methyl-2-buten-1-ol (321-mb) and 3-methyl-2-buten-1-al dehydrogenases, suggesting that 232-mb is metabolized by isomerization to 321-mb followed by oxidation. 321-mb dehydrogenase was purified to near-hom ...	1999	10347052
effect of organic solvents on the yield of solvent-tolerant pseudomonas putida s12.	solvent-tolerant microorganisms are useful in biotransformations with whole cells in two-phase solvent-water systems. the results presented here describe the effects that organic solvents have on the growth of these organisms. the maximal growth rate of pseudomonas putida s12, 0.8 h-1, was not affected by toluene in batch cultures, but in chemostat cultures the solvent decreased the maximal growth rate by nearly 50%. toluene, ethylbenzene, propylbenzene, xylene, hexane, and cyclohexane reduced t ...	1999	10347053
cis/trans isomerase of unsaturated fatty acids of pseudomonas putida p8: evidence for a heme protein of the cytochrome c type.	from a pool of 600 temperature-sensitive transposon mutants of pseudomonas putida p8, 1 strain was isolated that carries a mini-tn5 insertion within the cytochrome c operon. as a result, genes involved in the attachment of heme to cytochrome c-type proteins are turned off. accordingly, cytochrome c could not be detected spectrophotometrically. the mutant also exhibited a remarkable reduction of cis-trans isomerization capability for unsaturated fatty acids. consistent with the genetic and physio ...	1999	10347055
characterization of the meta-cleavage compound hydrolase gene involved in degradation of the lignin-related biphenyl structure by sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 has the ability to transform a lignin-related biphenyl compound, 2,2'-dihydroxy-3,3'-dimethoxy-5, 5'-dicarboxybiphenyl (ddva), to 5-carboxyvanillic acid (5cva) via 2, 2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (oh-ddva). in the 4.9-kb hindiii fragment containing the oh-ddva meta-cleavage dioxygenase gene (ligz), we found a novel hydrolase gene (ligy) responsible for the conversion of the meta-cleavage compound of oh-ddva to 5cva. incorporation of 18o from h ...	1999	10347082
isolation and characterization of two cryptic plasmids in the ammonia-oxidizing bacterium nitrosomonas sp. strain eni-11.	two plasmids were discovered in the ammonia-oxidizing bacterium nitrosomonas sp. strain eni-11, which was isolated from activated sludge. the plasmids, designated pays and payl, were relatively small, being approximately 1.9 kb long. they were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. the complete nucleotide sequences of pays and payl were determined, and their physical maps were constructed. there existed two major open readin ...	1999	10348848
cloning and characterization of the genes encoding a cytochrome p450 (pipa) involved in piperidine and pyrrolidine utilization and its regulatory protein (pipr) in mycobacterium smegmatis mc2155.	transposon mutagenesis of mycobacterium smegmatis mc2155 enabled the isolation of a mutant strain (called lgm1) altered in the regulation of piperidine and pyrrolidine utilization. the complete nucleotide sequence of the gene inactivated in mutant lgm1 was determined from the wild-type strain. this gene (pipr) encoded a member of the gntr family of bacterial regulatory proteins. an insertion element (is1096), previously described for m. smegmatis, was detected downstream of the gene pipr. three ...	1999	10348853
a functional 4-hydroxysalicylate/hydroxyquinol degradative pathway gene cluster is linked to the initial dibenzo-p-dioxin pathway genes in sphingomonas sp. strain rw1.	the bacterium sphingomonas sp. strain rw1 is able to use dibenzo-p-dioxin, dibenzofuran, and several hydroxylated derivatives as sole sources of carbon and energy. we have determined and analyzed the nucleic acid sequence of a 9,997-bp hindiii fragment downstream of cistrons dxna1a2, which encode the dioxygenase component of the initial dioxygenase system of the corresponding catabolic pathways. this fragment contains 10 colinear open reading frames (orfs), apparently organized in one compact op ...	1999	10348858
regulation of alginate biosynthesis in pseudomonas syringae pv. syringae.	both pseudomonas aeruginosa and the phytopathogen p. syringae produce the exopolysaccharide alginate. however, the environmental signals that trigger alginate gene expression in p. syringae are different from those in p. aeruginosa with copper being a major signal in p. syringae. in p. aeruginosa, the alternate sigma factor encoded by algt (sigma22) and the response regulator algr1 are required for transcription of algd, a gene which encodes a key enzyme in the alginate biosynthetic pathway. in ...	1999	10348861
genetic analysis of a chromosomal region containing vana and vanb, genes required for conversion of either ferulate or vanillate to protocatechuate in acinetobacter.	vana and vanb form an oxygenative demethylase that converts vanillate to protocatechuate in microorganisms. ferulate, an abundant phytochemical, had been shown to be metabolized through a vanillate intermediate in several pseudomonas isolates, and biochemical evidence had indicated that vanillate also is an intermediate in ferulate catabolism by acinetobacter. genetic evidence supporting this conclusion was obtained by characterization of mutant acinetobacter strains blocked in catabolism of bot ...	1999	10348863
the physiological contribution of acinetobacter pcak, a transport system that acts upon protocatechuate, can be masked by the overlapping specificity of vank.	vank is the fourth member of the ubiquitous major facilitator superfamily of transport proteins to be identified that, together with pcak, benk, and muck, contributes to aromatic catabolism in acinetobacter sp. strain adp1. vank and pcak have overlapping specificity for p-hydroxybenzoate and, most clearly, for protocatechuate: inactivation of both proteins severely impairs growth with protocatechuate, and the activity of either protein alone can mask the phenotype associated with inactivation of ...	1999	10348864
comparison of the heme iron utilization systems of pathogenic vibrios.	vibrio alginolyticus, vibrio fluvialis, and vibrio parahaemolyticus utilized heme and hemoglobin as iron sources and contained chromosomal dna similar to several vibrio cholerae heme iron utilization genes. a v. parahaemolyticus gene that performed the function of v. cholerae huta was isolated. a portion of the tonb1 locus of v. parahaemolyticus was sequenced and found to encode proteins similar in amino acid sequence to v. cholerae hutw, tonb1, and exbb1. a recombinant plasmid containing the v. ...	1999	10348876
cloning, sequence analysis, and expression of the pseudomonas putida 33/1 1h-3-hydroxy-4-oxoquinoline 2,4-dioxygenase gene, encoding a carbon monoxide forming dioxygenase.	1h-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (qdo) from the 1h-4-oxoquinoline utilizing pseudomonas putida strain 33/1, which catalyzes the cleavage of 1h-3-hydroxy-4-oxoquinoline to carbon monoxide and n-formylanthranilate, is devoid of any transition metal ion or other cofactor and thus represents a novel type of ring-cleavage dioxygenase. gene qdo was cloned and sequenced. its overexpression in escherichia coli yielded recombinant his-tagged qdo which was catalytically active. qdo exhibited 36 ...	1999	10350631
characterization of a novel cis-benzene dihydrodiol dehydrogenase from pseudomonas putida ml2.	a second and novel cis-benzene dihydrodiol dehydrogenase which is able to dehydrogenate a range of cis-dihydrodiols and other vicinal alcohols has been purified from pseudomonas putida ml2. the enzyme is a tetramer of a polypeptide of 39 kda in molecular mass and has a ph optimum of 9.0. despite having a primary structure that has significant similarity to glycerol dehydrogenases, the kcat/km value of the enzyme for cis-benzene dihydrodiol is 4300-fold higher compared to glycerol. the apparent k ...	1999	10356973
pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases.	coronatine, syringomycin, syringopeptin, tabtoxin, and phaseolotoxin are the most intensively studied phytotoxins of pseudomonas syringae, and each contributes significantly to bacterial virulence in plants. coronatine functions partly as a mimic of methyl jasmonate, a hormone synthesized by plants undergoing biological stress. syringomycin and syringopeptin form pores in plasma membranes, a process that leads to electrolyte leakage. tabtoxin and phaseolotoxin are strongly antimicrobial and func ...	1999	10357851
pas domains: internal sensors of oxygen, redox potential, and light.	pas domains are newly recognized signaling domains that are widely distributed in proteins from members of the archaea and bacteria and from fungi, plants, insects, and vertebrates. they function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. specificity in sensing arises, in part, from different cofactors that may be associated with the pas fold. transduction of redox signals may be a common mechanistic theme in many different pas domains. pas pr ...	1999	10357859
genetic organization of sulphur-controlled aryl desulphonation in pseudomonas putida s-313.	pseudomonas putida s-313 is able to desulphonate a broad range of aromatic sulphonates to provide sulphur for growth by monooxygenolytic cleavage to yield the corresponding phenol. after minitn5 transposon mutagenesis of this strain, 11 mutants were isolated that were no longer able to utilize benzenesulphonate as a sulphur source. three of these mutants were defective in the utilization of all aromatic sulphonates tested, but they grew normally with other sulphur sources. these strains containe ...	1999	10361295
bacterioferritin a modulates catalase a (kata) activity and resistance to hydrogen peroxide in pseudomonas aeruginosa.	we have cloned a 3.6-kb genomic dna fragment from pseudomonas aeruginosa harboring the rpoa, rplq, kata, and bfra genes. these loci are predicted to encode, respectively, (i) the alpha subunit of rna polymerase; (ii) the l17 ribosomal protein; (iii) the major catalase, kata; and (iv) one of two iron storage proteins called bacterioferritin a (bfra; cytochrome b1 or b557). our goal was to determine the contributions of kata and bfra to the resistance of p. aeruginosa to hydrogen peroxide (h2o2). ...	1999	10368148
a mutant escherichia coli primase defective in elongation of primer rna chains.	earlier we showed by affinity cross-linking of initiating substrates to escherichia coli primase that one or more of the residues lys211, lys229, and lys241 were involved in the catalytic center of the enzyme (a. a. mustaev and g. n. godson, j. biol. chem. 270:15711-15718, 1995). we now demonstrate by mutagenesis that only lys241 but not lys211 and lys229 is part of the catalytic center. primase with a mutation of arg to lys at position 241 (defined as k241r-primase) is almost unable to synthesi ...	1999	10368151
biochemical and molecular characterization of the bacillus subtilis acetoin catabolic pathway.	a recent study indicated that bacillus subtilis catabolizes acetoin by enzymes encoded by the acu gene cluster (f. j. grundy, d. a. waters, t. y. takova, and t. m. henkin, mol. microbiol. 10:259-271, 1993) that are completely different from those in the multicomponent acetoin dehydrogenase enzyme system (aodh es) encoded by aco gene clusters found before in all other bacteria capable of utilizing acetoin as the sole carbon source for growth. by hybridization with a dna probe covering acoa and ac ...	1999	10368162
an archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from ppseudomonas putida mt-2.	catechol dioxygenases catalyze the ring cleavage of catechol and its derivatives in either an intradiol or extradiol manner. these enzymes have a key role in the degradation of aromatic molecules in the environment by soil bacteria. catechol 2, 3-dioxygenase catalyzes the incorporation of dioxygen into catechol and the extradiol ring cleavage to form 2-hydroxymuconate semialdehyde. catechol 2,3-dioxygenase (metapyrocatechase, mpc) from pseudomonas putida mt-2 was the first extradiol dioxygenase ...	1999	10368270
cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase and cis-1, 2-dihydro-1,2-dihydroxynaphathalene dehydrogenase catalyze dehydrogenation of the same range of substrates.	pseudomonas putida strain g7 cis-1,2-dihydro-1, 2-dihydroxynaphthalene dehydrogenase (nahb) and comamonas testosteroni strain b-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (bphb) were found to be catalytically active towards cis-2,3-dihydro-2,3-dihydroxybiphenyl (specificity factors of 501 and 5850 s-1 mm-1 respectively), cis-1,2-dihydro-1, 2-dihydroxynaphthalene (specificity factors of 204 and 193 s-1 mm-1 respectively) and 3,4-dihydro-3,4-dihydroxy-2,2',5, 5'-tetrachlorobiphenyl (s ...	1999	10381363
effect of rpos mutation on the stress response and expression of virulence factors in pseudomonas aeruginosa.	the sigma factor rpos (sigmas) has been described as a general stress response regulator that controls the expression of genes which confer increased resistance to various stresses in some gram-negative bacteria. to elucidate the role of rpos in pseudomonas aeruginosa physiology and pathogenesis, we constructed rpos mutants in several strains of p. aeruginosa, including pao1. the pao1 rpos mutant was subjected to various environmental stresses, and we compared the resistance phenotype of the mut ...	1999	10383954
characterization of the major superoxide dismutase of staphylococcus aureus and its role in starvation survival, stress resistance, and pathogenicity.	a staphylococcus aureus mutant (spw1) which is unable to survive long-term starvation was shown to have a transposon insertion within a gene homologous to the soda family of manganese-dependent superoxide dismutases (sod). whole-cell lysates of the parental 8325-4 strain demonstrated three zones of sod activity by nondenaturing gel electrophoresis. the activities of two of these zones were dependent on manganese for activity and were absent in spw1. the levels of sod activity and soda expression ...	1999	10383955
ribonucleotide reduction in pseudomonas species: simultaneous presence of active enzymes from different classes.	three separate classes of ribonucleotide reductases exist in nature. they differ widely in protein structure. class i enzymes are found in aerobic bacteria and eukaryotes; class ii enzymes are found in aerobic and anaerobic bacteria; class iii enzymes are found in strict and facultative anaerobic bacteria. usually, but not always, one organism contains only one or two (in facultative anaerobes) classes. surprisingly, the genomic sequence of pseudomonas aeruginosa contains sequences for each of t ...	1999	10383965
temperature-sensitive motility of sulfolobus acidocaldarius influences population distribution in extreme environments.	a three-dimensional tracking microscope was used to quantify the effects of temperature (50 to 80 degrees c) and ph (2 to 4) on the motility of sulfolobus acidocaldarius, a thermoacidophilic archaeon. swimming speed and run time increased with temperature but remained relatively unchanged with increasing ph. these results were consistent with reported changes in the rate of respiration of s. acidocaldarius as a function of temperature and ph. cells exhibited a forward-biased turn angle distribut ...	1999	10383970
the pvc gene cluster of pseudomonas aeruginosa: role in synthesis of the pyoverdine chromophore and regulation by ptxr and pvds.	a putative operon of four genes implicated in the synthesis of the chromophore moiety of the pseudomonas aeruginosa siderophore pyoverdine, dubbed pvcabcd (where pvc stands for pyoverdine chromophore), was cloned and sequenced. mutational inactivation of the pvc genes abrogated pyoverdine biosynthesis, consistent with their involvement in the biosynthesis of this siderophore. pvcabcd expression was negatively regulated by iron and positively regulated by both pvds, the alternate sigma factor req ...	1999	10383985
laboratory evolution of peroxide-mediated cytochrome p450 hydroxylation.	enzyme-based chemical transformations typically proceed with high selectivity under mild conditions, and are becoming increasingly important in the pharmaceutical and chemical industries. cytochrome p450 monooxygenases (p450s) constitute a large family of enzymes of particular interest in this regard. their biological functions, such as detoxification of xenobiotics and steroidogenesis, are based on the ability to catalyse the insertion of oxygen into a wide variety of compounds. such a catalyti ...	1999	10385118
an outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process.	activated sludge was fed phenol as the sole carbon source, and the phenol-loading rate was increased stepwise from 0.5 to 1.0 g liter-1 day-1 and then to 1.5 g liter-1 day-1. after the loading rate was increased to 1.5 g liter-1 day-1, nonflocculating bacteria outgrew the sludge, and the activated-sludge process broke down within 1 week. the bacterial population structure of the activated sludge was analyzed by temperature gradient gel electrophoresis (tgge) of pcr-amplified 16s ribosomal dna (r ...	1999	10388669
quantification of chemotaxis to naphthalene by pseudomonas putida g7.	the capillary assay was used to quantify the chemotactic response of pseudomonas putida g7 to naphthalene. experiments were conducted in which the cell concentration in the assay chamber, the naphthalene concentration in the capillary, or the incubation time was varied. data from these experiments were evaluated with a model that accounted for the effect of diffusion on the distribution of substrate and the transport of cells from the chamber through the capillary orifice. by fitting a numerical ...	1999	10388674
identification and sequencing of beta-myrcene catabolism genes from pseudomonas sp. strain m1.	the m1 strain, able to grow on beta-myrcene as the sole carbon and energy source, was isolated by an enrichment culture and identified as a pseudomonas sp. one beta-myrcene-negative mutant, called n22, obtained by transposon mutagenesis, accumulated (e)-2-methyl-6-methylen-2,7-octadien-1-ol (or myrcen-8-ol) as a unique beta-myrcene biotransformation product. this compound was identified by gas chromatography-mass spectrometry. we cloned and sequenced the dna regions flanking the transposon and u ...	1999	10388678
physiological adaptations involved in alkane assimilation at a low temperature by rhodococcus sp. strain q15.	we examined physiological adaptations which allow the psychrotroph rhodococcus sp. strain q15 to assimilate alkanes at a low temperature (alkanes are contaminants which are generally insoluble and/or solid at low temperatures). during growth at 5 degrees c on hexadecane or diesel fuel, strain q15 produced a cell surface-associated biosurfactant(s) and, compared to glucose-acetate-grown cells, exhibited increased cell surface hydrophobicity. a transmission electron microscopy examination of strai ...	1999	10388690
composition of toluene-degrading microbial communities from soil at different concentrations of toluene.	toluene-degrading bacteria were isolated from hydrocarbon-contaminated soil by incubating liquid enrichment cultures and agar plate cultures in desiccators in which the vapor pressure of toluene was controlled by dilution with vacuum pump oil. incubation in desiccators equilibrated with either 100, 10, or 1% (wt/wt) toluene in vacuum pump oil and testing for genomic cross-hybridization resulted in four genomically distinct strains (standards) capable of growth on toluene (strains cstd1, cstd2, c ...	1999	10388704
why metronidazole is active against both bacteria and parasites.		1999	10390199
activation of the 2'-n-acetyltransferase gene [aac(2')-ia] in providencia stuartii by an interaction of aarp with the promoter region.	the aac(2')-ia gene in providencia stuartii encodes a 2'-n-acetyltransferase capable of acetylating both peptidoglycan and certain aminoglycoside antibiotics. regulation of the aac(2')-ia gene is influenced in a positive manner by the product of the aarp gene, which encodes a small transcriptional activator of the arac (xyls) family. in this study, we demonstrate the sequence requirements at the aac(2')-ia promoter for aarp binding and activation.	1999	10390241
development of a bioconversion process for production of cis-1s,2r-indandiol from indene by recombinant escherichia coli constructs.	recombinant escherichia coli cells expressing the toluene dioxygenase (tdo) genes from pseudomonas putida convert indene to cis-1s,2r-indandiol, a potentially important intermediate for the chemical synthesis of the hiv-1 protease inhibitor, crixivan. a bioconversion process was developed through optimization of medium composition and reaction conditions at the shake-flask and 23-1 fermentor scales. a cis-1,2-indandiol productivity of approx. 1000 mg/l was achieved with construct tdo123, which r ...	1999	10390819
a comparison between toxicity tests using single species and a microbial process.	in this study the sensitivity of the acetate mineralization process performed by five strains of microorganisms in soil for the toxicants zn2+ or pcp was calculated from the sensitivity of the contributing species. the species used were a fungus (aspergillus niger cbs 121.49), an actinomycete (streptomyces lividans 66), two gram-negative pseudomonas putida strains (mt-2 and dsm 50026) and a gram-positive strain rhodococcus erythropolis a177. for zinc the ec10 of the process performed by the five ...	1999	10390842
use of a monoclonal antibody against an escherichia coli o26 surface protein for detection of enteropathogenic and enterohemorrhagic strains.	a monoclonal antibody (mab) was obtained from a mouse immunized with solubilized outer membrane proteins extracted from a bovine enterohemorrhagic strain of escherichia coli (ehec), o26. the mab produced a strong immunoblot reaction at approximately 21 kda for an o26 strain containing the intimin gene (eae) and verocytotoxin (vt), but not with an o26 eae- and vt-negative strain, or o157 eae- and vt-positive strains. the mab was used in a sandwich enzyme-linked immunosorbent assay (elisa) format ...	1999	10391872
structure of the soluble methane monooxygenase regulatory protein b.	the soluble methane monooxygenase (smmo; ec 1.14.13.25) from the pseudothermophile methylococcus capsulatus (bath) is a three-component enzyme system that catalyzes the selective oxidation of methane to methanol. we have used nmr spectroscopy to produce a highly refined structure of mmob, the 16-kda regulatory protein of this system. this structure has a unique and intricate fold containing seven beta-strands forming two beta-sheets oriented perpendicular to each other and bridged by three alpha ...	1999	10393915
biodegradability of cefotiam, ciprofloxacin, meropenem, penicillin g, and sulfamethoxazole and inhibition of waste water bacteria	most antibiotics are metabolized only incompletely by patients after administration and enter the municipal sewage with the patients' excretions. little is known about their biodegradability in aquatic environments and their role with respect to growing bacterial resistance. therefore, the biodegradability of some clinically important antibiotic drugs as a very first step of an environmental risk assessment was investigated with the oecd closed bottle test (cbt). to assess toxicity of the test c ...	1999	10398765
isolation and characterization of mutations in the escherichia coli regulatory protein xapr.	in this work, the lysr-type protein xapr has been subjected to a mutational analysis. xapr regulates the expression of xanthosine phosphorylase (xapa), a purine nucleoside phosphorylase in escherichia coli. in the wild type, full expression of xapa requires both a functional xapr protein and the inducer xanthosine. here we show that deoxyinosine can also function as an inducer in the wild type, although not to the same extent as xanthosine. we have isolated and characterized in detail the mutant ...	1999	10400599
gene silencing via protein-mediated subcellular localization of dna.	we previously reported that overexpression of sopb, an escherichia coli f plasmid-encoded partition protein, led to silencing of genes linked to, but well-separated from, a cluster of sopb-binding sites termed sopc. we show here that in this sopb-mediated repression of sopc-linked genes, all but the n-terminal 82 amino acids of sopb can be replaced by the dna-binding domain of a sequence-specific dna-binding protein, provided that the sopc locus is also replaced by the recognition sequence of th ...	1999	10411914
copurification of the fpva ferric pyoverdin receptor of pseudomonas aeruginosa with its iron-free ligand: implications for siderophore-mediated iron transport.	the pseudomonas aeruginosa fpva receptor is a tonb-dependent outer membrane transport protein that catalyzes uptake of ferric pyoverdin across the outer membrane. surprisingly, fpva expressed in p. aeruginosa grown in an iron-deficient medium copurifies with a ligand x that we have characterized by uv, fluorescence, and mass spectrometry as being iron-free pyoverdin (apo-paa). paa was absent from fpva purified from a paa-deficient p. aeruginosa strain. the properties of ligand binding in vitro r ...	1999	10413510
development of environmentally friendly coatings and paints using medium-chain-length poly(3-hydroxyalkanoates) as the polymer binder.	unsaturated medium-chain-length poly(3-hydroxyalkanoates) (mcl-phas) produced by pseudomonas putida from linseed oil fatty acids (lofa) and tall oil fatty acids (tofa), were used as the polymer binder in the formulation of high solid alkyd-like paints. the relatively high concentration of unsaturated alkyl side chains incorporated into the pha resins resulted in oxidative drying pha paints having excellent coating properties. the homogeneously pigmented pha coatings yielded high-gloss, smooth an ...	1999	10416658
role of tolr n-terminal, central, and c-terminal domains in dimerization and interaction with tola and tolq.	the tol-pal system of escherichia coli is a multiprotein system involved in maintaining the cell envelope integrity and is necessary for the import of some colicins and phage dna into the bacterium. it is organized into two complexes, one near the outer membrane between tolb and pal and one in the cytoplasmic membrane between tola, tolq, and tolr. in the cytoplasmic membrane, all of the tol proteins have been shown to interact with each other. cross-linking experiments have shown that the tola t ...	1999	10419942
outer membrane changes in a toluene-sensitive mutant of toluene-tolerant pseudomonas putida ih-2000.	we isolated a toluene-sensitive mutant, named mutant no. 32, which showed unchanged antibiotic resistance levels, from toluene-tolerant pseudomonas putida ih-2000 by transposon mutagenesis with tn5. the gene disrupted by insertion of tn5 was identified as cyoc, which is one of the subunits of cytochrome o. the membrane protein, phospholipid, and lipopolysaccharide (lps) of ih-2000 and that of mutant no. 32 were examined and compared. some of the outer membrane proteins showed a decrease in mutan ...	1999	10419944
areabc genes determine the catabolism of aryl esters in acinetobacter sp. strain adp1.	acinetobacter sp. strain adp1 is able to grow on a range of esters of aromatic alcohols, converting them to the corresponding aromatic carboxylic acids by the sequential action of three inducible enzymes: an area-encoded esterase, an areb-encoded benzyl alcohol dehydrogenase, and an arec-encoded benzaldehyde dehydrogenase. the are genes, adjacent to each other on the chromosome and transcribed in the order arecba, were located 3.5 kbp upstream of benk. benk, encoding a permease implicated in ben ...	1999	10419955
a zymomonas mobilis mutant with delayed growth on high glucose concentrations.	exponentially growing cells of zymomonas mobilis normally exhibit a lag period of up to 3 h when transferred from 0.11 m (2%) to 0.55 m (10%) glucose liquid medium. a mutant of z. mobilis (cu1rif2), fortuitously isolated, showed more than a 20-h lag period when grown under the same conditions, whereas on 0.55 m glucose solid medium, it failed to grow. the growth of cu1rif2 on elevated concentrations of other fermentable (0.55 m sucrose or fructose) or nonfermentable (0.11 m glucose plus 0.44 m m ...	1999	10419959
mgatp binding and hydrolysis determinants of ntrc, a bacterial enhancer-binding protein.	when phosphorylated, the dimeric form of nitrogen regulatory protein c (ntrc) of salmonella typhimurium forms a larger oligomer(s) that can hydrolyze atp and hence activate transcription by the sigma(54)-holoenzyme form of rna polymerase. studies of mg-nucleoside triphosphate binding using a filter-binding assay indicated that phosphorylation is not required for nucleotide binding but probably controls nucleotide hydrolysis per se. studies of binding by isothermal titration calorimetry indicated ...	1999	10419963
[effect of arsenite on the physiological and cytological properties of pseudomonas putida strains capable of degrading polycyclic aromatic hydrocarbons].	some physiological and cytological properties of pseudomonas putida strains resistant to arsenite and capable of degrading polycyclic aromatic hydrocarbons were studied. the resistance of p. putida bs202 (npl-1) to arsenite proved to be determined by chromosomal genes, while the arsenite resistance of p. putida bs238 (pbs2; pbs3031) was by plasmid-borne genes. arsenite affected the pattern and rate of growth of strain bs202 (npl-1) in media with naphthalene or salicylate as carbon sources; parti ...	1999	10420398
solid matrix characterization of immobilized pseudomonas putida mtcc 1194 used for phenol degradation.	characterization studies of calcium alginate beads with encapsulated pseudomonas putida mtcc 1194, used for the biodegradation of phenol, were carried out to investigate the reactivity, reusability and structural strength of the solid matrix. various techniques were employed to improve the structural stability of the immobilized solid necessary for its use in commercial reactors like packed bed flow reactor, fluidized bed and cstr systems. experiments were performed to establish the optimum cond ...	1999	10422235
crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes.	the family of giant multienzyme complexes metabolizing pyruvate, 2-oxoglutarate, branched-chain 2-oxo acids or acetoin contains several of the largest and most sophisticated protein assemblies known, with molecular masses between 4 and 10 million da. the principal enzyme components, e1, e2 and e3, are present in numerous copies and utilize multiple cofactors to catalyze a directed sequence of reactions via substrate channeling. the crystal structure of a heterotetrameric (alpha2beta2) e1, 2-oxoi ...	1999	10426958
engineering of stable recombinant bacteria for production of chiral medium-chain-length poly-3-hydroxyalkanoates.	in order to scale up medium-chain-length polyhydroxyalkanoate (mcl-pha) production in recombinant microorganisms, we generated and investigated different recombinant bacteria containing a stable regulated expression system for phac1, which encodes one of the mcl-pha polymerases of pseudomonas oleovorans. we used the mini-tn5 system as a tool to construct escherichia coli 193mc1 and p. oleovorans pomc1, which had stable antibiotic resistance and pha production phenotypes when they were cultured i ...	1999	10427005
degradation of 3-phenoxybenzoic acid in soil by pseudomonas pseudoalcaligenes pob310(ppob) and two modified pseudomonas strains.	pseudomonas pseudoalcaligenes pob310(ppob) and pseudomonas sp. strains b13-d5(pd30.9) and b13-st1(ppob) were introduced into soil microcosms containing 3-phenoxybenzoic acid (3-pob) in order to evaluate and compare bacterial survival, degradation of 3-pob, and transfer of plasmids to a recipient bacterium. strain pob310 was isolated for its ability to use 3-pob as a growth substrate; degradation is initiated by pob-dioxygenase, an enzyme encoded on ppob. strain b13-d5 contains pd30.9, a cloning ...	1999	10427019
heat-induced expression and chemically induced expression of the escherichia coli stress protein htpg are affected by the growth environment.	differences in expression of the escherichia coli stress protein htpg were found following exposure of exponentially growing cells to heat or chemical shock when cells were grown under different environmental conditions. with an htpg::lacz reporter system, htpg expression increased in cells grown in a complex medium (luria-bertani [lb] broth) following a temperature shock at 45 degrees c. in contrast, no htpg overexpression was detected in cells grown in a glucose minimal medium, despite a decre ...	1999	10427031
factors influencing expression of luxcdabe and nah genes in pseudomonas putida rb1353(nah7, putk9) in dynamic systems.	bioluminescent reporter organisms have been successfully exploited as analytical tools for in situ determination of bioavailable levels of contaminants in static environmental samples. continued characterization and development of such reporter systems is needed to extend the application of these bioreporters to in situ monitoring of degradation in dynamic environmental systems. in this study, the naphthalene-degrading, lux bioreporter bacterium pseudomonas putida rb1353 was used to evaluate the ...	1999	10427037
community analysis of biofilters using fluorescence in situ hybridization including a new probe for the xanthomonas branch of the class proteobacteria.	domain-, class-, and subclass-specific rrna-targeted probes were applied to investigate the microbial communities of three industrial and three laboratory-scale biofilters. the set of probes also included a new probe (named xan818) specific for the xanthomonas branch of the class proteobacteria; this probe is described in this study. the members of the xanthomonas branch do not hybridize with previously developed rrna-targeted oligonucleotide probes for the alpha-, beta-, and gamma-proteobacteri ...	1999	10427047
cloning, molecular analysis, and expression of the polyhydroxyalkanoic acid synthase (phac) gene from chromobacterium violaceum.	the polyhydroxyalkanoic acid synthase gene from chromobacterium violaceum (phac(cv)) was cloned and characterized. a 6.3-kb bamhi fragment was found to contain both phac(cv) and the polyhydroxyalkanoic acid (pha)-specific 3-ketothiolase (phaa(cv)). escherichia coli strains harboring this fragment produced significant levels of pha synthase and 3-ketothiolase, as judged by their activities. while c. violaceum accumulated poly(3-hydroxybutyrate) or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) when ...	1999	10427049
microbial population changes during bioremediation of an experimental oil spill.	three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. in situ microbial community structures were monitored by phospholipid fatty acid (plfa) analysis and 16s rdna pcr-denaturing gradient gel electrophoresis (dgge) to (i) identify the bacterial community members responsible for the decontamination ...	1999	10427050
regiospecificity of dioxygenation of di- to pentachlorobiphenyls and their degradation to chlorobenzoates by the bph-encoded catabolic pathway of burkholderia sp. strain lb400.	burkholderia sp. strain lb400 is one of the most potent aerobic polychlorobiphenyl (pcb)-degrading microorganisms that have been characterized. its pcb-dioxygenating activity originates predominantly or exclusively from the biphenyl dioxygenase encoded by its bph gene cluster. analysis of the dioxygenation products of several di- to pentachlorinated biphenyls formed by this enzyme revealed a complex dependence of the regiospecificity and the yield of dioxygenation on the substitution patterns of ...	1999	10427057
high rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis.	quantitative in situ determination of conjugative gene transfer in defined bacterial biofilms using automated confocal laser scanning microscopy followed by three-dimensional analysis of cellular biovolumes revealed conjugation rates 1,000-fold higher than those determined by classical plating techniques. conjugation events were not affected by nutrient concentration alone but were influenced by time and biofilm structure.	1999	10427070
the branched-chain dodecylbenzene sulfonate degradation pathway of pseudomonas aeruginosa w51d involves a novel route for degradation of the surfactant lateral alkyl chain.	pseudomonas aeruginosa w51d is able to grow by using branched-chain dodecylbenzene sulfonates (b-dbs) or the terpenic alcohol citronellol as a sole source of carbon. a mutant derived from this strain (w51m1) is unable to degrade citronellol but still grows on b-dbs, showing that the citronellol degradation route is not the main pathway involved in the degradation of the surfactant alkyl moiety. the structures of the main b-dbs isomers and of some intermediates were identified by gas chromatograp ...	1999	10427075
replication origin region of the chromosome of alkaliphilic bacillus halodurans c-125.	an 18.5-kb dna fragment containing the oric region of the chromosome of the alkaliphilic bacillus halodurans c-125 was obtained by pcr and sequenced. sixteen open reading frames (orfs) were identified in this region. a sequencing similarity search using the bsorf database found that orf1 to 13 all had significant similarities to gene products of bacillus subtilis. three other orfs (orf14-16) of unknown function were positioned down-stream of gyrb instead of rrno, which is found in the same regio ...	1999	10427704
crystal structure and mechanism of co dehydrogenase, a molybdo iron-sulfur flavoprotein containing s-selanylcysteine.	co dehydrogenase from the aerobic bacterium oligotropha carboxidovorans catalyzes the oxidation of co with h(2)o, yielding co(2), two electrons, and two h(+). its crystal structure in the air-oxidized form has been determined to 2.2 a. the active site of the enzyme, which contains molybdenum with three oxygen ligands, molybdopterin-cytosine dinucleotide and s-selanylcysteine, delivers the electrons to an intramolecular electron transport chain composed of two types of [2fe-2s] clusters and flavi ...	1999	10430865
genome signature comparisons among prokaryote, plasmid, and mitochondrial dna.	our basic observation is that each genome has a characteristic "signature" defined as the ratios between the observed dinucleotide frequencies and the frequencies expected if neighbors were chosen at random (dinucleotide relative abundances). the remarkable fact is that the signature is relatively constant throughout the genome; i.e. , the patterns and levels of dinucleotide relative abundances of every 50-kb segment of the genome are about the same. comparison of the signatures of different gen ...	1999	10430917
rapid evaluation of biocidal activity using a transposon-encoded catechol 2,3-dioxygenase from pseudomonas putida.	pseudomonas putida (uwc1), containing a genetically-engineered plasmid (pqm899), that encodes for the production of catechol 2,3-dioxygenase (c230), was used as a potential means of rapidly estimating bactericidal activity of chlorhexidine diacetate (cha), phenol, cetylpyridinium chloride (cpc) and phenylmercuric nitrate (pmn). enzyme c230 converts catechol to 2-hydroxymuconic semialdehyde (2-hms), which is yellow in colour, via a meta cleavage pathway. ideal conditions for production and measur ...	1999	10432591
(s)-mandelate dehydrogenase from pseudomonas putida: mutations of the catalytic base histidine-274 and chemical rescue of activity.	(s)-mandelate dehydrogenase from pseudomonas putida, an fmn-dependent alpha-hydroxy acid dehydrogenase, oxidizes (s)-mandelate to benzoylformate. the generally accepted catalytic mechanism for this enzyme involves the formation of a carbanion intermediate. histidine-274 has been proposed to be the active-site base that abstracts the substrate alpha-proton to generate the carbanion. histidine-274 was altered to glycine, alanine, and asparagine. all three mutants were completely inactive. the muta ...	1999	10433701
heterologous expression and characterization of the purified oxygenase component of rhodococcus globerulus p6 biphenyl dioxygenase and of chimeras derived from it.	in this work, we have purified the his-tagged oxygenase (ht-oxygenase) component of rhodococcus globerulus p6 biphenyl dioxygenase. the alpha or beta subunit of p6 oxygenase was exchanged with the corresponding subunit of pseudomonas sp. strain lb400 or of comamonas testosteroni b-356 to create new chimeras that were purified ht-proteins and designated ht-alpha(p6)beta(p6), ht-alpha(p6)beta(lb400), ht-alpha(p6)beta(b-356), ht-alpha(lb400)beta(p6), and ht-alpha(b-356)beta(p6). ht-alpha(p6)beta(p6 ...	1999	10438748
catalytic properties of the 3-chlorocatechol-oxidizing 2, 3-dihydroxybiphenyl 1,2-dioxygenase from sphingomonas sp. strain bn6.	the 2,3-dihydroxybiphenyl dioxygenase from sphingomonas sp. strain bn6 (bphc1-bn6) differs from most other extradiol dioxygenases by its ability to oxidize 3-chlorocatechol to 3-chloro-2-hydroxymuconic semialdehyde by a distal cleavage mechanism. the turnover of different substrates and the effects of various inhibitors on bphc1-bn6 were compared with those of another 2,3-dihydroxybiphenyl dioxygenase from the same strain (bphc2-bn6) as well as with those of the archetypical catechol 2,3-dioxyge ...	1999	10438749
proton-nuclear magnetic resonance analyses of the substrate specificity of a beta-ketolase from pseudomonas putida, acetopyruvate hydrolase.	a revised purification of acetopyruvate hydrolase from orcinol-grown pseudomonas putida orc is described. this carbon-carbon bond hydrolase, which is the last inducible enzyme of the orcinol catabolic pathway, is monomeric with a molecular size of approximately 38 kda; it hydrolyzes acetopyruvate to equimolar quantities of acetate and pyruvate. we have previously described the aqueous-solution structures of acetopyruvate at ph 7.5 and several synthesized analogues by (1)h-nuclear magnetic resona ...	1999	10438778
conserved cytoplasmic loops are important for both the transport and chemotaxis functions of pcak, a protein from pseudomonas putida with 12 membrane-spanning regions.	chemotaxis to the aromatic acid 4-hydroxybenzoate (4-hba) by pseudomonas putida is mediated by pcak, a membrane-bound protein that also functions as a 4-hba transporter. pcak belongs to the major facilitator superfamily (mfs) of transport proteins, none of which have so far been implicated in chemotaxis. work with two well-studied mfs transporters, lacy (the lactose permease) and teta (a tetracycline efflux protein), has revealed two stretches of amino acids located between the second and third ...	1999	10438780
[non fermentative gram negative bacilli isolated in a hospital laboratory].	to report a prospective study on non fermentative gramnegative bacilli, excluded pseudomonas aeruginosa, isolated at dr. julio c. perrando hospital in resistencia (argentina). the goal of this study was to know their frequency and antimicrobial susceptibility.	1999	10439535
conjugative plasmid transfer between pseudomonas strains within alginate bead microcosms: effect of the internal gel structure.	because microorganisms frequently live in an immobilized state in natural habitats, a cell-confined system was used to study bacterial conjugation. two pseudomonas putida strains were introduced together within calcium alginate gels. different alginate beads were designed by varying the polysaccharide and the gelation solution concentrations. microscopic examinations showed that 2% gels were quite homogeneous, but that 1.5% and 1% gels were rather heterogeneous. in these two last cases, shaft-sh ...	1999	10440669
independent prediction of naphthalene transport and biodegradation in soil with a mathematical model.	experiments were performed to test the ability of a mathematical model to predict naphthalene transport and biodegradation. pseudomonas putida g7, a model bacterial strain capable of degrading naphthalene, was added to a column packed with the soil that had been pre-equilibrated with naphthalene. model prediction for transport and degradation were based on predetermined parameters that described naphthalene desorption kinetics and the utilization of naphthalene by the test bacterium. however, in ...	1999	10440672
role of ornibactin biosynthesis in the virulence of burkholderia cepacia: characterization of pvda, the gene encoding l-ornithine n(5)-oxygenase.	burkholderia cepacia is a frequent cause of respiratory infections in cystic fibrosis patients. b. cepacia has been shown to produce at least four siderophores which may play a role in the virulence of this organism. to characterize genes involved in the synthesis of siderophores, tn5-ot182 mutants were isolated in strain k56-2, which produces two siderophores, salicylic acid (sa) and ornibactins. two mutants were characterized that did not produce zones on chrome azurol s agar in a commonly use ...	1999	10456885
the gene locus yijp contributes to escherichia coli k1 invasion of brain microvascular endothelial cells.	most cases of escherichia coli meningitis develop as a result of hematogenous spread, but it is not clear how circulating e. coli crosses the blood-brain barrier. a tnphoa mutant of e. coli k1 rs218 was shown to be significantly less invasive than its parent strain in bovine and human brain microvascular endothelial cells (bmec), which constitute the blood-brain barrier. more importantly, traversal of the blood-brain barrier was significantly less with this mutant than with the parent strain in ...	1999	10456927
the espd protein of enterohemorrhagic escherichia coli is required for the formation of bacterial surface appendages and is incorporated in the cytoplasmic membranes of target cells.	the formation of espa-containing surface appendages in pathogenic escherichia coli strains, both enteropathogenic e. coli (epec) and shiga toxin-producing e. coli strains, is essential for critical events in the infective process, e.g., localized bacterial adherence to host cells with formation of microcolonies and induction of attaching and effacing lesions. it has been reported that epec mutants deficient in the production of espd, which is encoded by the esp operon, are unable to accumulate a ...	1999	10456938
evaluation of acyl coenzyme a oxidase (aox) isozyme function in the n-alkane-assimilating yeast yarrowia lipolytica.	we have identified five acyl coenzyme a (coa) oxidase isozymes (aox1 through aox5) in the n-alkane-assimilating yeast yarrowia lipolytica, encoded by the pox1 through pox5 genes. the physiological function of these oxidases has been investigated by gene disruption. single, double, triple, and quadruple disruptants were constructed. global aox activity was determined as a function of time after induction and of substrate chain length. single null mutations did not affect growth but affected the c ...	1999	10464181
amino acid-dna contacts by rhas: an arac family transcription activator.	rhas, an arac family protein, activates rhabad transcription by binding to rhai, a site consisting of two 17-bp inverted repeat half-sites. in this work, amino acids in rhas that make base-specific contacts with rhai were identified. sequence similarity with arac suggested that the first contacting motif of rhas was a helix-turn-helix. assays of rhab-lacz activation by alanine mutants within this potential motif indicated that residues 201, 202, 205, and 206 might contact rhai. the second motif ...	1999	10464186
the 17-gene ethanolamine (eut) operon of salmonella typhimurium encodes five homologues of carboxysome shell proteins.	the eut operon of salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. previous genetic analysis revealed six eut genes that are needed for aerobic use of ethanolamine; one (eutr), encodes a positive regulator which mediates induction of the operon by vitamin b12 plus ethanolamine. the dna sequence of the eut operon included 17 genes, suggesting a more complex pathway than that revealed genetically. we have correlated an open reading frame in t ...	1999	10464203
catabolism of branched-chain alpha-keto acids in enterococcus faecalis: the bkd gene cluster, enzymes, and metabolic route.	genes encoding a branched-chain alpha-keto acid dehydrogenase from enterococcus faecalis 10c1, e1alpha (bkda), e1beta (bkdb), e2 (bkdc), and e3 (bkdd), were found to reside in the gene cluster ptb-buk-bkddabc. the predicted products of ptb and buk exhibited significant homology to the phosphotransbutyrylase and butyrate kinase, respectively, from clostridium acetobutylicum. activity and redox properties of the purified recombinant enzyme encoded by bkdd indicate that e. faecalis has a lipoamide ...	1999	10464218
mutations affecting motifs of unknown function in the central domain of nitrogen regulatory protein c.	the positive control function of the bacterial enhancer-binding protein ntrc resides in its central domain, which is highly conserved among activators of sigma54 holoenzyme. previous studies of a small set of mutant forms specifically defective in transcriptional activation, called ntrc repressor [ntrc(rep)] proteins, had enabled us to locate various functional determinants in the central domain. in this more comprehensive survey, the dna encoding a major portion of the central domain was random ...	1999	10464219
identification of the omega4499 regulatory region controlling developmental expression of a myxococcus xanthus cytochrome p-450 system.	omega4499 is the site of a tn5 lac insertion in the myxococcus xanthus chromosome that fuses lacz expression to a developmentally regulated promoter. cell-cell interactions that occur during development, including c signaling, are required for normal expression of tn5 lac omega4499. the dna upstream of the omega4499 insertion has been cloned, and the promoter has been localized. analysis of the dna sequence downstream of the promoter revealed one complete open reading frame and a second partial ...	1999	10464222
crystal structure of pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: an enzyme involved in the tyrosine degradation pathway.	in plants and photosynthetic bacteria, the tyrosine degradation pathway is crucial because homogentisate, a tyrosine degradation product, is a precursor for the biosynthesis of photosynthetic pigments, such as quinones or tocophenols. homogentisate biosynthesis includes a decarboxylation step, a dioxygenation and a rearrangement of the pyruvate sidechain. this complex reaction is carried out by a single enzyme, the 4-hydroxyphenylpyruvate dioxygenase (hppd), a non-heme iron dependent enzyme that ...	1999	10467142
amplified fragment length polymorphism fingerprinting of pseudomonas strains from a poultry processing plant.	molecular typing has been used previously to identify and trace dissemination of pathogenic and spoilage bacteria associated with food processing. amplified fragment length polymorphism (aflp) is a novel dna fingerprinting technique which is considered highly reproducible and has high discriminatory power. this technique was used to fingerprint 88 pseudomonas fluorescens and pseudomonas putida strains that were previously isolated from plate counts of carcasses at six processing stages and vario ...	1999	10473382
occurrence of shewanella algae in danish coastal water and effects of water temperature and culture conditions on its survival.	the marine bacterium shewanella algae, which was identified as the cause of human cases of bacteremia and ear infections in denmark in the summers of 1994 and 1995, was detected in seawater only during the months (july, august, september, and october) when the water temperature was above 13 degrees c. the bacterium is a typical mesophilic organism, and model experiments were conducted to elucidate the fate of the organism under cold and nutrient-limited conditions. the culturable count of s. alg ...	1999	10473392
identification of the pseudomonas stutzeri ox1 toluene-o-xylene monooxygenase regulatory gene (tour) and of its cognate promoter.	toluene-o-xylene monooxygenase is an enzymatic complex, encoded by the touabcdef genes, responsible for the early stages of toluene and o-xylene degradation in pseudomonas stutzeri ox1. in order to identify the loci involved in the transcriptional regulation of the tou gene cluster, deletion analysis and complementation studies were carried out with pseudomonas putida paw340 as a heterologous host harboring pfb1112, a plasmid that allowed regulated expression, inducible by toluene and o-xylene a ...	1999	10473416
oxygen-sensing reporter strain of pseudomonas fluorescens for monitoring the distribution of low-oxygen habitats in soil.	the root-colonizing bacterium pseudomonas fluorescens cha0 was used to construct an oxygen-responsive biosensor. an anaerobically inducible promoter of pseudomonas aeruginosa, which depends on the fnr (fumarate and nitrate reductase regulation)-like transcriptional regulator anr (anaerobic regulation of arginine deiminase and nitrate reductase pathways), was fused to the structural lacz gene of escherichia coli. by inserting the reporter fusion into the chromosomal atttn7 site of p. fluorescens ...	1999	10473420
distribution of bacterial growth activity in flow-chamber biofilms.	in microbial communities such as those found in biofilms, individual organisms most often display heterogeneous behavior with respect to their metabolic activity, growth status, gene expression pattern, etc. in that context, a novel reporter system for monitoring of cellular growth activity has been designed. it comprises a transposon cassette carrying fusions between the growth rate-regulated escherichia coli rrnbp1 promoter and different variant gfp genes. it is shown that the p1 promoter is r ...	1999	10473423
identification of nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase.	immunoblot analyses performed with three monoclonal antibodies (mabs) that recognized the nitrite oxidoreductase (nor) of the genus nitrobacter were used for taxonomic investigations of nitrite oxidizers. we found that these mabs were able to detect the nitrite-oxidizing systems (nos) of the genera nitrospira, nitrococcus, and nitrospina. the mab designated hyb 153-2, which recognized the alpha subunit of the nor (alpha-nor), was specific for species belonging to the genus nitrobacter. in contra ...	1999	10473425
impact of rpos deletion on escherichia coli biofilms.	slow growth has been hypothesized to be an essential aspect of bacterial physiology within biofilms. in order to test this hypothesis, we employed two strains of escherichia coli, zk126 (deltalacz rpos(+)) and its isogenic deltarpos derivative, zk1000. these strains were grown at two rates (0.033 and 0.0083 h(-1)) in a glucose-limited chemostat which was coupled either to a modified robbins device containing plugs of silicone rubber urinary catheter material or to a glass flow cell. the presence ...	1999	10473455
metabolism and genetics of helicobacter pylori: the genome era.	the publication of the complete sequence of helicobacter pylori 26695 in 1997 and more recently that of strain j99 has provided new insight into the biology of this organism. in this review, we attempt to analyze and interpret the information provided by sequence annotations and to compare these data with those provided by experimental analyses. after a brief description of the general features of the genomes of the two sequenced strains, the principal metabolic pathways are analyzed. in particu ...	1999	10477311
controlled specific expression and purification of 6 x his-tagged proteins in pseudomonas.	the 6 x his affinity tags have proved invaluable for the exclusive purification of proteins, in escherichia coli, of genes cloned in frame with a 6 x his tag and a strong inducible promoter. here, we demonstrate that the system can be extended to gram-negative bacteria other than e. coli, by the use of compatible broad-host-range plasmids. as an example, the inducible synthesis and specific purification of the pseudomonas 6 x his-pfra siderophore regulatory protein in pseudomonas putida wcs358 i ...	1999	10481093