| fructosebisphosphatase isoenzymes of the chemoautotroph xanthobacter flavus. | xanthobacter flavus employs two fructosebisphosphatase (fbpase)-sedoheptulosebisphosphatase (sbpase) enzymes. one of these is constitutively expressed and has a high fbpase-to-sbpase ratio. the alternative enzyme, which is encoded by cbbf, is induced during autotrophic growth. the cbbf gene was expressed in escherichia coli, and the fbpase was purified to homogeneity. the purified enzyme has a specific fbpase activity of 114 mumol/min/mg of protein, a michaelis constant for fructosebisphosphate ... | 1995 | 7592335 |
| the calvin cycle enzyme phosphoglycerate kinase of xanthobacter flavus required for autotrophic co2 fixation is not encoded by the cbb operon. | during autotrophic growth of xanthobacter flavus, energy derived from the oxidation of hydrogen methanol or formate is used to drive the assimilation of co2 via the calvin cycle. the genes encoding the calvin cycle enzymes are organized in the cbb operon, which is expressed only during autotrophic growth. although it has been established that the transcriptional activator cbbr is required for the expression of the cbb operon, it is unclear whether cbbr is the only factor contributing to the regu ... | 1994 | 7928974 |
| cbbr, a lysr-type transcriptional activator, is required for expression of the autotrophic co2 fixation enzymes of xanthobacter flavus. | xanthobacter flavus is able to grow autotrophically with the enzymes of the calvin cycle for the fixation of co2, which are specified by the cbblsxfp gene cluster. previously, the 5' end of an open reading frame (cbbr), displaying a high sequence similarity to the lysr family of regulatory proteins and transcribed divergently from cbblsxfp, was identified (w. g. meijer, a. c. arnberg, h. g. enequist, p. terpstra, m. e. lidstrom, and l. dijkhuizen, mol. gen. genet. 225:320-330, 1991). this paper ... | 1993 | 8407781 |
| expression and regulation of bradyrhizobium japonicum and xanthobacter flavus co2 fixation genes in a photosynthetic bacterial host. | calvin cycle carbon dioxide fixation genes encoded on dna fragments from two nonphotosynthetic, chemolithoautotrophic bacteria, bradyrhizobium japonicum and xanthobacter flavus, were found to complement and support photosynthetic growth of a ribulose 1,5-bisphosphate carboxylase-oxygenase (rubisco) deletion mutant of the purple nonsulfur bacterium rhodobacter sphaeroides. the regulation of rubisco expression was analyzed in the complemented r. sphaeroides rubisco deletion mutant. distinct differ ... | 1993 | 8423157 |
| degradation of 1,4-dichlorobenzene by xanthobacter flavus 14p1. | xanthobacter flavus 14p1 was isolated from sludge of the river mulde by selective enrichment with 1,4-dichlorobenzene as the sole source of carbon and energy. the bacterium did not use other aromatic or chloroaromatic compounds as growth substrates. during growth on 1,4-dichlorobenzene, stoichiometric amounts of chloride ions were released. degradation products of 1,4-dichlorobenzene were identified by gas chromatography-mass spectrometry analysis. 3,6-dichloro-cis-1,2-dihydroxycyclohexa-3,5-die ... | 1995 | 8526500 |
| induction of the gap-pgk operon encoding glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase of xanthobacter flavus requires the lysr-type transcriptional activator cbbr. | in a previous study, a gene (pgk) encoding phosphoglycerate kinase was isolated from a genomic library of xanthobacter flavus. although this gene is essential for autotrophic growth, it is not located within the cbb operon encoding other calvin cycle enzymes. an analysis of the nucleotide sequence upstream from pgk showed the presence of a gene encoding glyceraldehyde-3-phosphate dehydrogenase and the 3' end of an open reading frame encoding a protein which is 50% identical to transketolase enco ... | 1996 | 8550526 |
| primary structure and phylogeny of the calvin cycle enzymes transketolase and fructosebisphosphate aldolase of xanthobacter flavus. | xanthobacter flavus, a gram-negative facultatively autotrophic bacterium, employs the calvin cycle for the fixation of carbon dioxide. cells grown under autotrophic growth conditions possess an fe(2+)-dependent fructosebisphosphate (fbp) aldolase (class ii) in addition to a class i fbp aldolase. by nucleotide sequencing and heterologous expression in escherichia coli, genes encoding transketolase (ec 2.2.1.1.; cbbt) and class ii fbp aldolase (ec 4.1.2.13; cbba) were identified. a partial open re ... | 1996 | 8550527 |
| the lysr-type transcriptional regulator cbbr controlling autotrophic co2 fixation by xanthobacter flavus is an nadph sensor. | autotrophic growth of xanthobacter flavus is dependent on the fixation of carbon dioxide via the calvin cycle and on the oxidation of simple organic and inorganic compounds to provide the cell with energy. maximal induction of the cbb and gap-pgk operons encoding enzymes of the calvin cycle occurs in the absence of multicarbon substrates and the presence of methanol, formate, hydrogen, or thiosulfate. the lysr-type transcriptional regulator cbbr regulates the expression of the cbb and gap-pgk op ... | 1998 | 9515907 |
| physiological control and regulation of the rhodobacter capsulatus cbb operons. | the genes encoding enzymes of the calvin-benson-bassham (cbb) reductive pentose phosphate pathway in rhodobacter capsulatus are organized in at least two operons, each preceded by a separate cbbr gene, encoding potential lysr-type transcriptional activators. as a prelude to studies of cbb gene regulation in r. capsulatus, the nucleotide sequence of a 4,537-bp region, which included cbbrii, was determined. this region contained the following open reading frames: a partial pgm gene (encoding phosp ... | 1998 | 9696777 |
| two functionally distinct regions upstream of the cbbi operon of rhodobacter sphaeroides regulate gene expression. | a number of cbbfi::lacz translational fusion plasmids containing various lengths of sequence 5' to the form i (cbbi) calvin-benson-bassham cycle operon (cbbficbbpicbbaicbblicbbsi) of rhodobacter sphaeroides were constructed. expression of beta-galactosidase was monitored under a variety of growth conditions. it was found that 103 bp of sequence upstream of the cbbfi transcription start was sufficient to confer low levels of regulated cbbi promoter expression; this activity was dependent on the p ... | 1998 | 9733694 |
| toxic effects of modified fenton reactions on xanthobacter flavus fb71 | the toxic effects of modified fenton reactions on xanthobacter flavus fb71, measured as microbial survival rates, were determined as part of an investigation of simultaneous abiotic and biotic oxidations of xenobiotic chemicals. a central composite, rotatable experimental design was developed to study the survival rates of x. flavus under various concentrations of hydrogen peroxide and iron(ii) and at different initial cell populations. a model based on the experimental results, relating microor ... | 1998 | 9758796 |
| degradation of 1,2,3,4-tetrachlorobenzene by pseudomonas chlororaphis rw71 | pseudomonas chlororaphis rw71 mineralized 1,2,3,4-tetrachlorobenzene, a highly recalcitrant pollutant hitherto not known to be degraded by pure cultures, as a sole source of carbon and energy, thereby releasing stoichiometric amounts of chloride. the transient excretion of tetrachlorocatechol in the early growth phase suggests an initial attack by a dioxygenase to form the corresponding dihydrodiol which rearomatizes to the catechol. the activity of chlorocatechol 1,2-dioxygenase in crude cell e ... | 1998 | 9758802 |
| degradation of chlorobenzenes at nanomolar concentrations by burkholderia sp. strain ps14 in liquid cultures and in soil. | the utilization of 1,2,4,5-tetrachloro-, 1,2,4-trichloro-, the three isomeric dichlorobenzenes and fructose as the sole carbon and energy sources at nanomolar concentrations was studied in batch experiments with burkholderia sp. strain ps14. in liquid culture, all chlorobenzenes were metabolized within 1 h from their initial concentration of 500 nm to below their detection limits of 0.5 nm for 1,2,4,5-tetrachloro- and 1,2,4-trichlorobenzene and 7.5 nm for the three dichlorobenzene isomers, with ... | 1999 | 10347041 |
| optimization of simultaneous chemical and biological mineralization of perchloroethylene. | optimization of the simultaneous chemical and biological mineralization of perchloroethylene (pce) by modified fenton's reagent and xanthobacter flavus was investigated by using a central composite rotatable experimental design. concentrations of pce, hydrogen peroxide, and ferrous iron and the microbial cell number were set as variables. percent mineralization of pce to co2 was investigated as a response. a second-order, quadratic response surface model was generated and fit the data adequately ... | 1999 | 10347081 |
| an additional regulatory gene for actinorhodin production in streptomyces lividans involves a lysr-type transcriptional regulator. | the sequence of a 4.8-kbp dna fragment adjacent to the right-hand end of the actinorhodin biosynthetic (act) cluster downstream of actvb-orf6 from streptomyces coelicolor a3(2) reveals six complete open reading frames, named orf7 to orf12. the deduced amino acid sequences from orf7, orf10, and orf11 show significant similarities with the following products in the databases: a putative protein from the s. coelicolor scp3 plasmid, lysr-type transcriptional regulators, and proteins belonging to the ... | 1999 | 10400594 |
| distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. | the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ... | 1999 | 10482517 |
| effects of the calvin cycle on nicotinamide adenine dinucleotide concentrations and redox balances of xanthobacter flavus. | the levels of reduced and oxidized nicotinamide adenine dinucleotides were determined in xanthobacter flavus during a transition from heterotrophic to autotrophic growth. excess reducing equivalents are rapidly dissipated following induction of the calvin cycle, indicating that the calvin cycle serves as a sink for excess reducing equivalents. the physiological data support the conclusion previously derived from molecular studies in that expression of the calvin cycle genes is controlled by the ... | 2000 | 10913100 |
| chlorocatechols substituted at positions 4 and 5 are substrates of the broad-spectrum chlorocatechol 1,2-dioxygenase of pseudomonas chlororaphis rw71. | the nucleotide sequence of a 10,528-bp region comprising the chlorocatechol pathway gene cluster tetrtetcdef of the 1,2,3,4-tetrachlorobenzene via the tetrachlorocatechol-mineralizing bacterium pseudomonas chlororaphis rw71 (t. potrawfke, k. n. timmis, and r.-m. wittich, appl. environ. microbiol. 64:3798-3806, 1998) was analyzed. the chlorocatechol 1,2-dioxygenase gene tetc was cloned and overexpressed in escherichia coli. the recombinant gene product was purified, and the alpha,alpha-homodimeri ... | 2001 | 11208799 |
| evidence that a linear megaplasmid encodes enzymes of aliphatic alkene and epoxide metabolism and coenzyme m (2-mercaptoethanesulfonate) biosynthesis in xanthobacter strain py2. | the bacterial metabolism of propylene proceeds by epoxidation to epoxypropane followed by a sequence of three reactions resulting in epoxide ring opening and carboxylation to form acetoacetate. coenzyme m (2-mercaptoethanesulfonic acid) (com) plays a central role in epoxide carboxylation by serving as the nucleophile for epoxide ring opening and the carrier of the c(3) unit that is ultimately carboxylated to acetoacetate, releasing com. in the present work, a 320-kb linear megaplasmid has been i ... | 2001 | 11244054 |
| phylogeny and functional expression of ribulose 1,5-bisphosphate carboxylase/oxygenase from the autotrophic ammonia-oxidizing bacterium nitrosospira sp. isolate 40ki. | the autotrophic ammonia-oxidizing bacteria (aob), which play an important role in the global nitrogen cycle, assimilate co(2) by using ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco). here we describe the first detailed study of rubisco (cbb) genes and proteins from the aob. the cbbls genes from nitrosospira sp. isolate 40ki were cloned and sequenced. partial sequences of the rubisco large subunit (cbbl) from 13 other aob belonging to the beta and gamma subgroups of the class proteobac ... | 2002 | 11751824 |
| metabolic signals that lead to control of cbb gene expression in rhodobacter capsulatus. | various mutant strains were used to examine the regulation and metabolic control of the calvin-benson-bassham (cbb) reductive pentose phosphate pathway in rhodobacter capsulatus. previously, a ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco)-deficient strain (strain sbi/ii) was found to show enhanced levels of cbb(i) and cbb(ii) promoter activities during photoheterotrophic growth in the presence of dimethyl sulfoxide. with this strain as the starting point, additional mutations were ma ... | 2002 | 11889097 |
| novel methylotrophy genes of methylobacterium extorquens am1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase. | ten novel methylotrophy genes of the facultative methylotroph methylobacterium extorquens am1 were identified from a transposon mutagenesis screen. one of these genes encodes a product having identity with dihydrofolate reductase (dhfr). this mutant has a c(1)-defective and methanol-sensitive phenotype that has previously only been observed for strains defective in tetrahydromethanopterin (h(4)mpt)-dependent formaldehyde oxidation. these results suggest that this gene, dmra, may encode dihydrome ... | 2003 | 12511515 |
| mrna differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species. | mrna differential display has been used to identify cyclohexanone oxidation genes in a mixed microbial community derived from a wastewater bioreactor. thirteen dna fragments randomly amplified from the total rna of an enrichment subculture exposed to cyclohexanone corresponded to genes predicted to be involved in the degradation of cyclohexanone. nine of these dna fragments are part of genes encoding three distinct baeyer-villiger cyclohexanone monooxygenases from three different bacterial speci ... | 2003 | 12514013 |
| qscr, a lysr-type transcriptional regulator and cbbr homolog, is involved in regulation of the serine cycle genes in methylobacterium extorquens am1. | a new gene, qscr, encoding a lysr-type transcriptional regulator that is a homolog of cbbr, has been characterized from the facultative methylotroph methylobacterium extorquens am1 and shown to be the major regulator of the serine cycle, the specific c1 assimilation pathway. the qscr mutant was shown to be unable to grow on c1 compounds, and it lacked the activity of serine-glyoxylate aminotransferase, a key enzyme of the serine cycle. activities of other serine cycle enzymes were decreased duri ... | 2003 | 12562792 |
| analysis of dna binding and transcriptional activation by the lysr-type transcriptional regulator cbbr of xanthobacter flavus. | the lysr-type transcriptional regulator cbbr controls the expression of the cbb and gap-pgk operons in xanthobacter flavus, which encode the majority of the enzymes of the calvin cycle required for autotrophic co2 fixation. the cbb operon promoter of this chemoautotrophic bacterium contains three potential cbbr binding sites, two of which partially overlap. site-directed mutagenesis and subsequent analysis of dna binding by cbbr and cbb promoter activity were used to show that the potential cbbr ... | 2003 | 12562794 |
| complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph nitrosomonas europaea. | nitrosomonas europaea (atcc 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. nitrosomonas europaea participates in the biogeochemical n cycle in the process of nitrification. its genome consists of a single circular chromosome of 2,812,094 bp. the gc skew analysis indicates that the genome is divided into two unequal replichores. genes are distributed evenly around the genome, with approximate ... | 2003 | 12700255 |
| a novel sensor of nadh/nad+ redox poise in streptomyces coelicolor a3(2). | we describe the identification of rex, a novel redox-sensing repressor that appears to be widespread among gram-positive bacteria. in streptomyces coelicolor rex binds to operator (rop) sites located upstream of several respiratory genes, including the cydabcd and rex-hemacd operons. the dna-binding activity of rex appears to be controlled by the redox poise of the nadh/nad+ pool. using electromobility shift and surface plasmon resonance assays we show that nadh, but not nad+, inhibits the dna-b ... | 2003 | 12970197 |
| use of borate to control the 5'-position-selective microbial glucosylation of pyridoxine. | nearly 100% 5'-position selectivity of transglucosylation from maltodextrin to pyridoxine (pn) by cells of verticillium dahliae tpu 4900 was observed when the reaction was carried out with borate. the same effect of borate was observed not only during synthesis of pyridoxine 5'-alpha-d-glucoside by partially purified enzyme of this strain but also during synthesis of this compound by other microorganisms and with other enzymes (alpha-glucosidase and cyclomaltodextrin glucanotransferase). the eff ... | 2003 | 14660349 |
| plasmid-dependent methylotrophy in thermotolerant bacillus methanolicus. | bacillus methanolicus can efficiently utilize methanol as a sole carbon source and has an optimum growth temperature of 50 degrees c. with the exception of mannitol, no sugars have been reported to support rapid growth of this organism, which is classified as a restrictive methylotroph. here we describe the dna sequence and characterization of a 19,167-bp circular plasmid, designated pbm19, isolated from b. methanolicus mga3. sequence analysis of pbm19 demonstrated the presence of the methanol d ... | 2004 | 14973041 |
| the lysr-type transcriptional regulator virr is required for expression of the virulence gene vapa of rhodococcus equi atcc 33701. | the virulence of the intracellular pathogen rhodococcus equi in foals is dependent on the presence of an 81-kb virulence plasmid encoding the virulence protein vapa. expression of this protein is induced by exposure to oxidative stress, high temperatures, and low phs, which reflect the conditions encountered by r. equi when it enters the host environment. the aim of this study was to determine whether the lysr-type transcriptional regulator virr, which is encoded by the virulence plasmid, is req ... | 2004 | 15317761 |
| co2-responsive expression and gene organization of three ribulose-1,5-bisphosphate carboxylase/oxygenase enzymes and carboxysomes in hydrogenovibrio marinus strain mh-110. | hydrogenovibrio marinus strain mh-110, an obligately lithoautotrophic hydrogen-oxidizing bacterium, fixes co2 by the calvin-benson-bassham cycle. strain mh-110 possesses three different sets of genes for ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco): cbbls-1 and cbbls-2, which belong to form i (l8s8), and cbbm, which belongs to form ii (lx). in this paper, we report that the genes for cbbls-1 (cbbls-1) and cbbm (cbbm) are both followed by the cbbqo genes and preceded by the cbbr gene ... | 2004 | 15317772 |
| effector-mediated interaction of cbbri and cbbrii regulators with target sequences in rhodobacter capsulatus. | in rhodobacter capsulatus, genes encoding enzymes of the calvin-benson-bassham reductive pentose phosphate pathway are located in the cbb(i) and cbb(ii) operons. each operon contains a divergently transcribed lysr-type transcriptional activator (cbbr(i) and cbbr(ii)) that regulates the expression of its cognate cbb promoter in response to an as yet unidentified effector molecule(s). both cbbr(i) and cbbr(ii) were purified, and the ability of a variety of potential effector molecules to induce ch ... | 2004 | 15547275 |
| diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbl) in differently managed agricultural soils. | a pcr-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) form i large-subunit genes (cbbl) as a functional marker of autotrophic bacteria that fix carbon dioxide via the calvin-benson-bassham cycle. we constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbl genes. the diversity of these cbbl genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. ... | 2005 | 15640185 |
| identification of clinically relevant viridans streptococci by an oligonucleotide array. | viridans streptococci (vs) are common etiologic agents of subacute infective endocarditis and are capable of causing a variety of pyogenic infections. many species of vs are difficult to differentiate by phenotypic traits. an oligonucleotide array based on 16s-23s rrna gene intergenic spacer (its) sequences was developed to identify 11 clinically relevant vs. these 11 species were streptococcus anginosus, s. constellatus, s. gordonii, s. intermedius, s. mitis, s. mutans, s. oralis, s. parasangui ... | 2005 | 15814960 |
| modulating dna bending affects nodd-mediated transcriptional control in rhizobium leguminosarum. | rhizobium leguminosarum nodd binds to the nod box of the inducible nod gene noda as a v-shaped tetramer and bends the nod box. in this work, we show that the nod gene inducer naringenin decreased gel mobility of nod box dna-nodd complexes by sharpening the nodd-induced dna bend, which correlated with noda transcription activation. nodd can induce different dna bends when the distance between the two half-sites of the nod box was modified, which severely affected nodd-mediated transcriptional con ... | 2005 | 15872217 |
| diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at rainbow springs, yellowstone national park. | in this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at rainbow springs, yellowstone national park. soil chemical analysis revealed high sulfate concentrations and low ph values (ph 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. the hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g., n-alkanes with chain lengths of c15 to c30, as well as branched alkanes, ... | 2005 | 16204508 |
| comparative study of the ability of three xanthobacter species to metabolize cycloalkanes. | the ability of three species of xanthobacter to metabolize cyclohexane and its derivatives has been compared. xanthobacter flavus was unable to utilize any of the cycloalkanes under investigation. x. autotrophicus was unable to utilize cyclohexane but was able to grow with a limited range of substituted cycloalkanes, including cyclohexanol and cyclohexanone. comparison of a previously isolated cyclohexane growing xanthobacter sp. with x. flavus and x. autotrophicus indicated it to be closely rel ... | 1986 | 16347162 |
| novel acetone metabolism in a propane-utilizing bacterium, gordonia sp. strain ty-5. | in the propane-utilizing bacterium gordonia sp. strain ty-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. in this study, the subsequent metabolism of acetone was studied. acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmab was cloned on the basis of the n-terminal amino acid sequences of acetone-induced proteins. the acma and acmb genes encode a baeyer-villiger monooxygenase (bvmo) and esterase, ... | 2007 | 17071761 |
| novel acetone metabolism in a propane-utilizing bacterium, gordonia sp. strain ty-5. | in the propane-utilizing bacterium gordonia sp. strain ty-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. in this study, the subsequent metabolism of acetone was studied. acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmab was cloned on the basis of the n-terminal amino acid sequences of acetone-induced proteins. the acma and acmb genes encode a baeyer-villiger monooxygenase (bvmo) and esterase, ... | 2007 | 17071761 |
| molecular mechanism of the regulation of bacillus subtilis gltab expression by gltc. | in bacillus subilis, glutamate synthase, a major enzyme of nitrogen metabolism, is encoded by the gltab operon. significant expression of this operon requires the activity of gltc, a lysr-family protein, encoded by the divergently transcribed gene. we purified a soluble, active form of gltc and found that it requires alpha-ketoglutarate, a substrate of glutamate synthase, to fully activate glta transcription in vitro, and that its activity is inhibited by glutamate, the product of glutamate synt ... | 2007 | 17134717 |
| molecular mechanism of the regulation of bacillus subtilis gltab expression by gltc. | in bacillus subilis, glutamate synthase, a major enzyme of nitrogen metabolism, is encoded by the gltab operon. significant expression of this operon requires the activity of gltc, a lysr-family protein, encoded by the divergently transcribed gene. we purified a soluble, active form of gltc and found that it requires alpha-ketoglutarate, a substrate of glutamate synthase, to fully activate glta transcription in vitro, and that its activity is inhibited by glutamate, the product of glutamate synt ... | 2007 | 17134717 |
| degradation of alkyl methyl ketones by pseudomonas veronii mek700. | pseudomonas veronii mek700 was isolated from a biotrickling filter cleaning 2-butanone-loaded waste air. the strain is able to grow on 2-butanone and 2-hexanol. the genes for degradation of short chain alkyl methyl ketones were identified by transposon mutagenesis using a newly designed transposon, mini-tn5495, and cloned in escherichia coli. dna sequence analysis of a 15-kb fragment revealed three genes involved in methyl ketone degradation. the deduced amino acid sequence of the first gene, me ... | 2007 | 17351032 |
| identification of medically important candida and non-candida yeast species by an oligonucleotide array. | the incidence of yeast infections has increased in the recent decades, with candida albicans still being the most common cause of infections. however, infections caused by less common yeasts have been widely reported in recent years. based on the internal transcribed spacer 1 (its 1) and its 2 sequences of the rrna genes, an oligonucleotide array was developed to identify 77 species of clinically relevant yeasts belonging to 16 genera. the its regions were amplified by pcr with a pair of fungus- ... | 2007 | 17507521 |
| the ancestor of the paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a nitrococcus-like gamma-proteobacterium. | paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living prochlorococcus and synechococcus species (ps-clade). members of the ps-clade of cyanobacteria contain a proteobacterial form 1a rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (hgt) of a carboxysomal operon. in rdna-phylogenies, the paulinella chromatophore diverged basal ... | 2007 | 17550603 |
| biodegradation of bis(2-chloroethyl) ether by xanthobacter sp. strain env481. | degradation of bis(2-chloroethyl) ether (bcee) was observed to occur in two bacterial strains. strain env481, a xanthobacter sp. strain, was isolated by enrichment culturing of samples from a superfund site located in the northeastern united states. the strain was able to grow on bcee or 2-chloroethylethyl ether as the sole source of carbon and energy. bcee degradation in strain env481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol ... | 2007 | 17873075 |
| increased catalytic efficiency following gene fusion of bifunctional methionine sulfoxide reductase enzymes from shewanella oneidensis. | methionine sulfoxide reductase enzymes msra and msrb have complementary stereospecificities that reduce the s and r stereoisomers of methionine sulfoxide (metso), respectively, and together function as critical antioxidant enzymes. in some pathogenic and metal-reducing bacteria, these genes are fused to form a bifunctional methionine sulfoxide reductase (i.e., msrba) enzyme. to investigate how gene fusion affects the substrate specificity and catalytic activities of msr, we have cloned and expre ... | 2007 | 17997579 |
| complete genome sequence of nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. | the complete genome of the ammonia-oxidizing bacterium nitrosospira multiformis (atcc 25196(t)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. gene homologs from nitrosomonas europaea and nitrosomonas eutropha were the best match f ... | 2008 | 18390676 |
| genes and pathways for co2 fixation in the obligate, chemolithoautotrophic acidophile, acidithiobacillus ferrooxidans, carbon fixation in a. ferrooxidans. | acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low ph (ph 1-2). although a substantial amount of information is available regarding co2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study. | 2010 | 20799944 |
| nucleus-independent control of the rubisco operon by the plastid-encoded transcription factor ycf30 in the red alga cyanidioschyzon merolae. | chloroplasts originated from a cyanobacterium, which was engulfed by a primitive eukaryotic host cell. during evolution, chloroplasts have largely lost their autonomy due to the loss of many genes from their own genomes. consequently, expression of genes encoded in the chloroplast genome is mainly controlled by the factors transferred from the cytosol to chloroplasts. however, chloroplast genomes of glaucophytes and red algae have retained some transcription factors (hypothetical chloroplast ope ... | 2010 | 20813908 |
| Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. | Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest so ... | 2011 | 21984248 |
| further unravelling the regulatory twist - metabolic coinducer-mediated cbbr-cbbi promoter interactions in rhodopseudomonas palustris cga010. | the cbb(i) region of rhodopseudomonas palustris contains the cbbls genes encoding form i ribulose -1, 5 -bisphosphate (rubp) carboxylase oxygenase (rubisco) along with a divergently transcribed regulator gene, cbbr. juxtaposed between cbbr and cbbls are the cbbrrs genes encoding an unusual three protein two-component (cbbrrs) system that modulates the ability of cbbr to influence cbbls expression. the nature of the metabolic signals that rps. palustris cbbr perceives to regulate cbbls transcript ... | 2012 | 22247506 |
| fructose degradation in the haloarchaeon haloferax volcanii involves a bacterial type phosphoenolpyruvate-dependent phosphotransferase system, fructose-1-phosphate kinase, and class ii fructose-1,6-bisphosphate aldolase. | the halophilic archaeon haloferax volcanii utilizes fructose as a sole carbon and energy source. genes and enzymes involved in fructose uptake and degradation were identified by transcriptional analyses, deletion mutant experiments, and enzyme characterization. during growth on fructose, the gene cluster hvo_1495 to hvo_1499, encoding homologs of the five bacterial phosphotransferase system (pts) components enzyme iib (eiib), enzyme i (ei), histidine protein (hpr), eiia, and eiic, was highly upr ... | 2012 | 22493022 |
| fingerprinting diazotroph communities in the chesapeake bay by using a dna macroarray. | investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on pcr amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifh. recent work has suggested that dna macroarrays provide semiquantitative fingerprints of diversity within mixtures of nifh amplicons (g. f. steward, b. d. jenkins, b. b. ward, and j. p. zehr, appl. environ. microbiol. 70:1455-1465 ... | 2004 | 15006803 |
| repertoire of free-living protozoa in contact lens solutions. | the repertoire of free-living protozoa in contact lens solutions is poorly known despite the fact that such protozoa may act as direct pathogens and may harbor intra-cellular pathogens. | 2016 | 27793130 |
| recovery of phenanthrene-degrading bacteria after simulated in situ persulfate oxidation in contaminated soil. | a continuous-flow column study was conducted to investigate the long-term effects of persulfate oxidation on the abundance and activity of the indigenous microbial community and phenanthrene-degrading bacteria in contaminated soil from a former manufactured gas plant (mgp) site. approximately six pore volumes of a 20 g/l persulfate solution were introduced into the column, followed by simulated groundwater for 500 days. soil samples were collected from the surface of the soil bed and along the c ... | 2010 | 21162560 |
| recovery of phenanthrene-degrading bacteria after simulated in situ persulfate oxidation in contaminated soil. | a continuous-flow column study was conducted to investigate the long-term effects of persulfate oxidation on the abundance and activity of the indigenous microbial community and phenanthrene-degrading bacteria in contaminated soil from a former manufactured gas plant (mgp) site. approximately six pore volumes of a 20 g/l persulfate solution were introduced into the column, followed by simulated groundwater for 500 days. soil samples were collected from the surface of the soil bed and along the c ... | 2010 | 21162560 |
| purification and characterization of phosphoribulokinase from the marine chromophytic alga heterosigma carterae. | in this study we characterized phosphoribulokinase (prk, ec 2.7.1. 19) from the eukaryotic marine chromophyte heterosigma carterae. serial column chromatography resulted in approximately 300-fold purification of the enzyme. a polypeptide of 53 kd was identified as prk by sequencing the amino terminus of the protein. this protein represents one of the largest composite monomers identified to date for any prk. the native holoenzyme demonstrated by flow performance liquid chromatography a molecular ... | 1998 | 9576802 |
| microcompartments in prokaryotes: carboxysomes and related polyhedra. | | 2001 | 11722879 |
| analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase. | a 492- to 495-bp fragment of the gene coding for the large subunit of the form i ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) (rbcl) was amplified by pcr from facultatively lithotrophic aerobic co-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic dna extracts from tephra and ash deposits from kilauea volcano, for which atmospheric co and hydrogen have been previously documented as important substrates. pcr products from the mats and volcanic site ... | 2004 | 15066819 |
| development and testing of a dna macroarray to assess nitrogenase (nifh) gene diversity. | a dna macroarray was developed and evaluated for its potential to distinguish variants of the dinitrogenase reductase (nifh) gene. diverse nifh gene fragments amplified from a clone library were spotted onto nylon membranes. amplified, biotinylated nifh fragments from individual clones or a natural picoplankton community were hybridized to the array and detected by chemiluminescence. a hybridization test with six individual targets mixed in equal proportions resulted in comparable relative signa ... | 2004 | 15006766 |
| the independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic calvin cycle. | in the calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (fbp) and sedoheptulose-1, 7-bisphosphate (sbp) are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (f/sbpase), while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (fbpase) and sedoheptulose-1, 7-bisphosphatase (sbpase), respectively. it was proposed that these two eukaryotic enzymes arose f ... | 2012 | 23083334 |
| dual role of ccpc protein in regulation of aconitase gene expression in listeria monocytogenes and bacillus subtilis. | the role of the ccpc regulatory protein as a repressor of the genes encoding the tricarboxylic acid branch enzymes of the krebs cycle (citrate synthase, citz; aconitase, citb; and isocitrate dehydrogenase, citc) has been established for both bacillus subtilis and listeria monocytogenes. in addition, hyperexpression of citb-lacz reporter constructs in an aconitase null mutant strain has been reported for b. subtilis. we show here that such hyperexpression of citb occurs in l. monocytogenes as wel ... | 2013 | 23139400 |
| removal of pharmaceuticals and personal care products during water recycling: microbial community structure and effects of substrate concentration. | many pharmaceuticals and personal care products (ppcps) have been shown to be biotransformed in water treatment systems. however, little research exists on the effect of initial ppcp concentration on ppcp biotransformation or on the microbial communities treating impacted water. in this study, biological ppcp removal at various concentrations was assessed using laboratory columns inoculated with wastewater treatment plant effluent. pyrosequencing was used to examine microbial communities in the ... | 2014 | 24509919 |
| autotrophic carbon dioxide fixation via the calvin-benson-bassham cycle by the denitrifying methanotroph "candidatus methylomirabilis oxyfera". | methane is an important greenhouse gas and the most abundant hydrocarbon in the earth's atmosphere. methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "candidatus methylomirabilis oxyfera" is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase react ... | 2014 | 24509918 |
| cbbr, the master regulator for microbial carbon dioxide fixation. | biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric co2 to be reduced to usable forms of organic carbon. this process, especially the calvin-bassham-benson (cbb) pathway of co2 fixation, provides the bulk of organic carbon found on earth. the enzyme ribulose 1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) performs the key and rate-limiting step whereby co2 is reduced and incorporated ... | 2015 | 26324454 |