| partial reconstruction of flavonoid and isoflavonoid biosynthesis in yeast using soybean type i and type ii chalcone isomerases. | flavonoids and isoflavonoids are major plant secondary metabolites that mediate diverse biological functions and exert significant ecological impacts. these compounds play important roles in many essential physiological processes. in addition, flavonoids and isoflavonoids have direct but complex effects on human health, ranging from reducing cholesterol levels and preventing certain cancers to improving women's health. in this study, we cloned and functionally characterized five soybean (glycine ... | 2005 | 15778463 |
| alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome p450 encoded on the nifd excision element of anabaena 7120. | alkanes have been hypothesized to act as universal inducers of bacterial cytochrome p450 gene expression. we tested this hypothesis on an unusual p450 gene (cyp110) found on a conserved 11 kilobase episomal dna element of unknown function found in filamentous cyanobacteria. we also monitored the binding of potential substrates to the p450 protein and explored the distribution of p450 protein in vegetative cells and nitrogen-fixing heterocysts using immuno-electron microscopy. | 2005 | 15790415 |
| transgenic expression of the soybean apyrase in lotus japonicus enhances nodulation. | the soybean apyrase, gs52, was previously characterized as an early nodulin that is expressed in roots and localized to the plasma membrane. transgenic lotus japonicus plants were constructed constitutively expressing the gs52 apyrase. segregation and southern-blot analysis identified four single-copy sense lines, several double-copy sense lines, and one double-copy antisense line for further analysis. the single- and double-copy sense gs52 l. japonicus lines had enhanced nodulation that correla ... | 2005 | 15793071 |
| gmn70 and ljn70. anion transporters of the symbiosome membrane of nodules with a transport preference for nitrate. | a cdna was isolated from soybean (glycine max) nodules that encodes a putative transporter (gmn70) of the major facilitator superfamily. gmn70 is expressed predominantly in mature nitrogen-fixing root nodules. by western-blot and immunocytochemical analyses, gmn70 was localized to the symbiosome membrane of infected root nodule cells, suggesting a transport role in symbiosis. to investigate its transport function, crna encoding gmn70 was expressed in xenopus laevis oocytes, and two-electrode vol ... | 2005 | 15793072 |
| the histidine of the c-type cytochrome cxxch haem-binding motif is essential for haem attachment by the escherichia coli cytochrome c maturation (ccm) apparatus. | c-type cytochromes are characterized by covalent attachment of haem to the protein by two thioether bonds formed between the haem vinyl groups and the cysteine sulphurs in a cxxch peptide motif. in escherichia coli and many other gram-negative bacteria, this post-translational haem attachment is catalysed by the ccm (cytochrome c maturation) system. the features of the apocytochrome substrate required and recognized by the ccm apparatus are uncertain. in the present study, we report investigatio ... | 2005 | 15801911 |
| functional insights from the distribution and role of homopeptide repeat-containing proteins. | expansion of "low complex" repeats of amino acids such as glutamine (poly-q) is associated with protein misfolding and the development of degenerative diseases such as huntington's disease. the mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (rcps) remains obscure, and the role (if any) of repeat regions remains to be determined. here, a web-accessible database of rcps is presented. the distribution and evolution of rcps t ... | 2005 | 15805494 |
| insights into heme-based o2 sensing from structure-function relationships in the fixl proteins. | fixl proteins are bacterial heme-containing signal transduction proteins responsible for sensing the o(2) concentration in the organism's environment. in sinorhizobium meliloti fixl is a protein histidine kinase that, together with its response regulator fixj, constitute an oxygen-sensitive switch for regulation of the organism's nitrogen fixation and microaerobic respiration genes. the o(2) sensitivity of the switch is such that it transitions during the process of symbiosis in alfalfa roots. b ... | 2005 | 15811514 |
| 6s rna is a widespread regulator of eubacterial rna polymerase that resembles an open promoter. | 6s rna is an abundant noncoding rna in escherichia coli that binds to sigma70 rna polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. we have computationally identified >100 new 6s rna homologs in diverse eubacterial lineages. two abundant bacillus subtilis rnas of unknown function (bsra and bsrb) and cyanobacterial 6sa rnas are now recognized as 6s homologs. structural probing of e. coli 6s rna and a b. subtilis homolo ... | 2005 | 15811922 |
| biocatalytic production of perillyl alcohol from limonene by using a novel mycobacterium sp. cytochrome p450 alkane hydroxylase expressed in pseudomonas putida. | a number of oxygenated monoterpenes present at low concentrations in plant oils have anticarcinogenic properties. one of the most promising compounds in this respect is (-)-perillyl alcohol. since this natural product is present only at low levels in a few plant oils, an alternative, synthetic source is desirable. screening of 1,800 bacterial strains showed that many alkane degraders were able to specifically hydroxylate l-limonene in the 7 position to produce enantiopure (-)-perillyl alcohol. t ... | 2005 | 15811996 |
| cloning, expression, and site-directed mutagenesis of the propene monooxygenase genes from mycobacterium sp. strain m156. | propene monooxygenase has been cloned from mycobacterium sp. strain m156, based on hybridization with the amoabcd genes of rhodococcus corallinus b276. sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that from r. corallinus b-276. attempts were made to express the pmoabcd operon in escherichia coli and mycobacterium smegmatis mc(2)155. in the former, there appeared to be a proble ... | 2005 | 15812019 |
| isolation and characterization of feca- and feob-mediated iron acquisition systems of the spirochete leptospira biflexa by random insertional mutagenesis. | the specific mechanisms by which leptospira spp. acquire iron from their ecological niches are unknown. a major factor contributing to our ignorance of spirochetal biology is the lack of methods for genetic analysis of these organisms. in this study, we have developed a system for random transposon mutagenesis of leptospira biflexa using a mariner transposon, himar1. to demonstrate the validity of himar1 in vivo transposon mutagenesis in l. biflexa, a screen of mutants for clones impaired in ami ... | 2005 | 15838052 |
| transcription activation in vitro by the bradyrhizobium japonicum regulatory protein fixk2. | in bradyrhizobium japonicum, the n2-fixing root nodule endosymbiont of soybean, a group of genes required for microaerobic, anaerobic, or symbiotic growth is controlled by fixk2, a key regulator that is part of the fixlj-fixk2 cascade. fixk2 belongs to the family of cyclic amp receptor protein/fumarate and nitrate reductase (crp/fnr) transcription factors that recognize a palindromic dna motif (crp/fnr box) associated with the regulated promoters. here, we report on a biochemical analysis of fix ... | 2005 | 15866917 |
| an adenylyl cyclase, cyab, acts as an osmosensor in myxococcus xanthus. | we have previously reported that a receptor-type adenylyl cyclase (cyaa) of myxococcus xanthus undergoes an osmosensor mainly during spore germination (y. kimura et al., j. bacteriol. 184:3578-3585, 2002). in the present study, we cloned another receptor-type adenylyl cyclase gene (cyab) and characterized the function of the cyab-encoded protein. disruption of cyab generates a mutant that showed growth retardation at high ionic (nacl) or high nonionic (sucrose) osmolarity. when vegetative cells ... | 2005 | 15866951 |
| utilization of the plant hormone indole-3-acetic acid for growth by pseudomonas putida strain 1290. | we have isolated from plant surfaces several bacteria with the ability to catabolize indole-3-acetic acid (iaa). one of them, isolate 1290, was able to utilize iaa as a sole source of carbon, nitrogen, and energy. the strain was identified by its 16s rrna sequence as pseudomonas putida. activity of the enzyme catechol 1,2-dioxygenase was induced during growth on iaa, suggesting that catechol is an intermediate of the iaa catabolic pathway. this was in agreement with the observation that the oxyg ... | 2005 | 15870323 |
| an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus. | dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ... | 2005 | 15886391 |
| diverse bacteria isolated from root nodules of phaseolus vulgaris and species within the genera campylotropis and cassia grown in china. | eighty bacterial isolates from root nodules of the leguminous plants phaseolus vulgaris, campylotropis spp. and cassia spp. grown in china were classified into five groups by phenotypic analyses, sds-page of whole-cell proteins, pcr-based 16s rrna gene restriction-fragment-length-polymorphism and sequencing. thirty-three isolates from the three plant genera were identified as agrobacterium tumefaciens because they are closely related to the type strain of a. tumefaciens. fourteen isolates from p ... | 2005 | 15900972 |
| purification and characterization of allophanate hydrolase (atzf) from pseudomonas sp. strain adp. | atzf, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. in the present study, the atzf gene from pseudomonas sp. strain adp was cloned and expressed as a his-tagged protein, and the protein was purified and characterized. atzf had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. the acti ... | 2005 | 15901697 |
| identification of a turnover element in region 2.1 of escherichia coli sigma32 by a bacterial one-hybrid approach. | induction of the heat shock response in escherichia coli requires the alternative sigma factor sigma32 (rpoh). the cellular concentration of sigma32 is controlled by proteolysis involving ftsh, other proteases, and the dnakj chaperone system. to identify individual sigma32 residues critical for degradation, we used a recently developed bacterial one-hybrid system and screened for stabilized versions of sigma32. the five single point mutations that rendered the sigma factor more stable mapped to ... | 2005 | 15901705 |
| prediction of functional modules based on comparative genome analysis and gene ontology application. | we present a computational method for the prediction of functional modules encoded in microbial genomes. in this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. we first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and gene ontology ass ... | 2005 | 15901854 |
| evaluation of the role of genes encoding for dehydrin proteins (lea d-11) during drought stress in arbuscular mycorrhizal glycine max and lactuca sativa plants. | in this study, it has been determined whether the arbuscular mycorrhizal (am) symbiosis is able to alter the pattern of dehydrin (lea d-11 group) transcript accumulation under drought stress, and whether such a possible alteration functions in the protection of the host plants against drought. two dehydrin-encoding genes have been cloned from glycine max (gmlea 8 and gmlea 10) and one from lactuca sativa (lslea 1) and they have been analysed for their contribution to the response against drought ... | 2005 | 15911559 |
| conserved modular design of an oxygen sensory/signaling network with species-specific output. | principles of modular design are evident in signaling networks that detect and integrate a given signal and, depending on the organism in which the network module is present, transduce this signal to affect different metabolic or developmental pathways. here we report a global transcriptional analysis of an oxygen sensory/signaling network in caulobacter crescentus consisting of the sensor histidine kinase fixl, its cognate response regulator fixj, the transcriptional regulator fixk, and the kin ... | 2005 | 15911751 |
| proteomic analysis of soybean root hairs after infection by bradyrhizobium japonicum. | infection of soybean root hairs by bradyrhizobium japonicum is the first of several complex events leading to nodulation. in the current proteomic study, soybean root hairs after inoculation with b. japonicum were separated from roots. total proteins were analyzed by two-dimensional (2-d) polyacrylamide gel electrophoresis. in one experiment, 96 protein spots were analyzed by matrix-assisted laser desorption ionization time-of-flight (maldi-tof) mass spectrometry (ms) to compare protein profiles ... | 2005 | 15915644 |
| effect of chlorimuron-ethyl on bradyrhizobium japonicum and its symbiosis with soybean. | possible side-effects of the acetolactate synthase (als)-inhibiting herbicide chlorimuron-ethyl on bradyrhizobium japonicum (kirchner & jordan) in pure culture and on inoculated soybean plants growing under controlled conditions were investigated. growth of b japonicum strain e109 was not affected by this herbicide even when exposed to concentrations 150 times higher than recommended field doses. however, nodulation of soybean plants treated 5 days after emergence with chlorimuron-ethyl at stand ... | 2005 | 15920784 |
| automatic selection of representative proteins for bacterial phylogeny. | although there are now about 200 complete bacterial genomes in genbank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. | 2005 | 15927057 |
| identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph acidithiobacillus ferrooxidans. | a cluster of five genes, proposed to be involved in the formation of extracellular polysaccharide (eps) precursors via the leloir pathway, have been identified in the acidophilic autotroph acidithiobacillus ferrooxidans. the order of the genes is luxa-gale-galk-pgm-galm, encoding a luxa-like protein, udp-glucose 4-epimerase, galactokinase, phosphoglucomutase, and galactose mutarotase, respectively. the gal cluster forms a single transcriptional unit and is therefore an operon. two other putative ... | 2005 | 15932984 |
| mutations in cytochrome assembly and periplasmic redox pathways in bordetella pertussis. | transposon mutagenesis of bordetella pertussis was used to discover mutations in the cytochrome c biogenesis pathway called system ii. using a tetramethyl-p-phenylenediamine cytochrome c oxidase screen, 27 oxidase-negative mutants were isolated and characterized. nine mutants were still able to synthesize c-type cytochromes and possessed insertions in the genes for cytochrome c oxidase subunits (ctac, -d, and -e), heme a biosynthesis (ctab), assembly of cytochrome c oxidase (sco2), or ferrochela ... | 2005 | 15937156 |
| identification of the omega4406 regulatory region, a developmental promoter of myxococcus xanthus, and a dna segment responsible for chromosomal position-dependent inhibition of gene expression. | when starved, myxococcus xanthus cells send signals to each other that coordinate their movements, gene expression, and differentiation. c-signaling requires cell-cell contact, and increasing contact brought about by cell alignment in aggregates is thought to increase c-signaling, which induces expression of many genes, causing rod-shaped cells to differentiate into spherical spores. c-signaling involves the product of the csga gene. a csga mutant fails to express many genes that are normally in ... | 2005 | 15937177 |
| recombinant pas-heme domains of oxygen sensing proteins: high level production and physical characterization. | details of a high-level recombinant production method for the heme-pas domains of heme oxygen sensing proteins from sinorhizobium meliloti (sm) (formerly rhizobium meliloti, rm), bradyrhizobium japonicum (bj), and escherichia coli (ec) are described. using a newly proposed, concise, and unambiguous naming system (also described here) these proteins are: smfixlh(128-264), bjfixlh(140-270), and ecdosh(1-147). in addition, high-level production of bjfixl(140-505), the soluble full-length protein co ... | 2005 | 15939306 |
| the tetr family of transcriptional repressors. | we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ... | 2005 | 15944459 |
| a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts. | analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. | 2005 | 15955239 |
| signature proteins that are distinctive of alpha proteobacteria. | the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group. | 2005 | 15960851 |
| the pleiotropic nature of symbiotic regulatory mutants: bradyrhizobium japonicum nifa gene is involved in control of nif gene expression and formation of determinate symbiosis. | in the slow-growing soybean symbiont, bradyrhizobium japonicum (strain 110), a nifa-like regulatory gene was located immediately upstream of the previously mapped fixa gene. by interspecies hybridization and partial dna sequencing the gene was found to be homologous to nifa from klebsiella pneumoniae and rhizobium meliloti, and to a lesser extent, also to ntrc from k. pneumoniae. the b. japonicum nifa gene product was shown to activate b. japonicum and k. pneumoniae nif promoters (using nif::lac ... | 1986 | 15966104 |
| characterization of a bifunctional puta homologue from bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor. | puta is a bifunctional flavoenzyme in bacteria that catalyzes the four-electron oxidation of proline to glutamate. in certain prokaryotes such as escherichia coli, puta is also a transcriptional repressor of the proline utilization (put) genes and thus is trifunctional. in this work, we have begun to assess differences between bifunctional and trifunctional puta enzymes by examining the puta protein from bradyrhizobium japonicum (bjputa). primary structure analysis of bjputa shows it lacks the d ... | 2005 | 15966737 |
| pyd genes of rhizobium sp. strain tal1145 are required for degradation of 3-hydroxy-4-pyridone, an aromatic intermediate in mimosine metabolism. | rhizobium sp. strain tal1145 degrades the leucaena toxin mimosine and its degradation product 3-hydroxy-4-pyridone (hp). the aim of this investigation is to characterize the rhizobium genes for hp degradation and transport. these genes were localized by subcloning and mutagenesis on a previously isolated cosmid, puhr263, containing mid genes of tal1145 required for mimosine degradation. two structural genes, pyda and pydb, encoding a metacleavage dioxygenase and a hydrolase, respectively, are re ... | 2005 | 15968058 |
| escherichia coli hypa is a zinc metalloprotein with a weak affinity for nickel. | the hyp operon encodes accessory proteins that are required for the maturation of the [nife] hydrogenase enzymes and, in some organisms, for the production of urease enzymes as well. hypa or a homologous protein is required for nickel insertion into the hydrogenase precursor proteins. in this study, recombinant hypa from escherichia coli was purified and characterized in vitro. metal analysis was used to demonstrate that hypa simultaneously binds stoichiometric zn(2+) and stoichiometric ni(2+). ... | 2005 | 15995183 |
| purification and characterization of a novel alcohol dehydrogenase from leifsonia sp. strain s749: a promising biocatalyst for an asymmetric hydrogen transfer bioreduction. | to find microorganisms that could reduce phenyl trifluoromethyl ketone (ptk) to (s)-1-phenyltrifluoroethanol [(s)-pte], styrene-assimilating bacteria (ca. 900 strains) isolated from soil samples were screened. we found that leifsonia sp. strain s749 was the most suitable strain for the conversion of ptk to (s)-pte in the presence of 2-propanol as a hydrogen donor. the enzyme corresponding to the reaction was purified homogeneity, characterized and designated leifsonia alcohol dehydrogenase (lsad ... | 2005 | 16000771 |
| l: -stereoselective amino acid amidase with broad substrate specificity from brevundimonas diminuta: characterization of a new member of the leucine aminopeptidase family. | brevundimonas diminuta tpu 5720 produces an amidase acting l-stereoselectively on phenylalaninamide. the enzyme (laaa(bd)) was purified to electrophoretic homogeneity by ammonium sulfate fractionation and four steps of column chromatography. the final preparation gave a single band on sds-page with a molecular weight of approximately 53,000. the native molecular weight of the enzyme was about 288,000 based on gel filtration chromatography, suggesting that the enzyme is active as a homohexamer. i ... | 2006 | 16001251 |
| origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. | we report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (aeps). this analysis greatly expands the range of diversity of the aeps and reveals the unique active site shared by all members of this superfamily. in particular, it is shown that eukaryotic nucleo-cytoplasmic large dna viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode aeps of a distinct family, which also includ ... | 2005 | 16027112 |
| variant tricarboxylic acid cycle in mycobacterium tuberculosis: identification of alpha-ketoglutarate decarboxylase. | mycobacterium tuberculosis (mtb) has adapted its metabolism for persistence in the human macrophage. the adaptations are likely to involve mtb's core intermediary metabolism, whose enzymes have been little studied. the tricarboxylic acid cycle is expected to yield precursors for energy, lipids, amino acids, and heme. the genome sequence of mtb h37rv predicts the presence of a complete tricarboxylic acid cycle, but we recently found that alpha-ketoglutarate dehydrogenase (kdh) activity is lacking ... | 2005 | 16027371 |
| the stringent response is required for amino acid and nitrate utilization, nod factor regulation, nodulation, and nitrogen fixation in rhizobium etli. | a rhizobium etli tn5 insertion mutant, lm01, was selected for its inability to use glutamine as the sole carbon and nitrogen source. the tn5 insertion in lm01 was localized to the rsh gene, which encodes a member of the rela/spot family of proteins. the lm01 mutant was affected in the ability to use amino acids and nitrate as nitrogen sources and was unable to accumulate (p)ppgpp when grown under carbon and nitrogen starvation, as opposed to the wild-type strain, which accumulated (p)ppgpp under ... | 2005 | 16030199 |
| iron-dependent cytochrome c1 expression is mediated by the status of heme in bradyrhizobium japonicum. | the heme prosthetic group of heme proteins contains iron, which can be a limiting nutrient. here, we show that cytochrome c1 protein from bradyrhizobium japonicum was strongly affected by the iron status, with low expression in cells grown under iron limitation. this control was not affected in mutants encoding the iron regulator irr or fur. furthermore, cytochrome c1 mrna was not influenced by the iron status, suggesting control at a posttranscriptional step. cytochrome c1 protein levels were v ... | 2005 | 16030200 |
| use of suppression-subtractive hybridization to identify genes in the burkholderia cepacia complex that are unique to burkholderia cenocepacia. | we have previously shown differences in virulence between species of the burkholderia cepacia complex using the alfalfa infection model and the rat agar bead chronic infection model. burkholderia cenocepacia strains were more virulent in these two infection models than burkholderia multivorans and burkholderia stabilis strains. in order to identify genes that may account for the increased virulence of b. cenocepacia, suppression-subtractive hybridization was performed between b. cenocepacia k56- ... | 2005 | 16030222 |
| de novo alanine synthesis by bacteroids of mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of lotus corniculatus. | deletion of both alanine dehydrogenase genes (alda) in mesorhizobium loti resulted in the loss of alda enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of lotus corniculatus plants. thus, neither indeterminate pea nodules nor determinate l. corniculatus nodules export alanine as the sole nitrogen secretion product. | 2005 | 16030244 |
| characterization of conformational changes coupled to ligand photodissociation from the heme binding domain of fixl. | using transient absorption spectroscopy and photoacoustic calorimetry (pac), we have characterized carbon monoxide photodissociation and rebinding to two forms of the heme domain of bradyrhizobium japonicum fixl. transient absorption results for the complete heme domain (fixl residues 140-270) and a truncated heme domain (missing 11 residues on the n-teminal end and 14 amino acid residues on the c-terminal end of the full length heme domain) show similar rates for ligand rebinding to the five-co ... | 2005 | 16042379 |
| characterization and calculation of a cytochrome c-cytochrome b5 complex using nmr data. | to identify the binding site for bovine cytochrome b(5) (cyt b(5)) on horse cytochrome c (cyt c), cross-saturation transfer nmr experiments were performed with (2)h- and (15)n-enriched cyt c and unlabeled cyt b(5). in addition, chemical shift changes of the cyt c backbone amide and side chain methyl resonances were monitored as a function of cyt b(5) concentration. the chemical shift changes indicate that the complex is in fast exchange, and are consistent with a 1:1 stoichiometry. a k(a) of (4 ... | 2005 | 16060674 |
| comparative analyses of codon and amino acid usage in symbiotic island and core genome in nitrogen-fixing symbiotic bacterium bradyrhizobium japonicum. | genes involved in the symbiotic interactions between the nitrogen-fixing endosymbiont bradyrhizobium japonicum, and its leguminous host are mostly clustered in a symbiotic island (si), acquired by the bacterium through a process of horizontal transfer. a comparative analysis of the codon and amino acid usage in core and si genes/proteins of b. japonicum has been carried out in the present study. the mutational bias, translational selection, and gene length are found to be the major sources of va ... | 2005 | 16060695 |
| carboxyl-terminal protease regulates brucella suis morphology in culture and persistence in macrophages and mice. | the putative carboxyl-terminal processing protease (ctpa) of brucella suis 1330 is a member of a novel family of endoproteases involved in the maturation of proteins destined for the cell envelope. the b. suis ctpa protein shared up to 77% homology with ctpa proteins of other bacteria. a ctpa-deficient brucella strain (1330deltactpa), generated by allelic exchange, produced smaller colonies on enriched agar plates and exhibited a 50% decrease in growth rate in enriched liquid medium and no growt ... | 2005 | 16077124 |
| two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, encode haloalkane dehalogenases with novel structures and substrate specificities. | haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, have open reading frames (orfs), mlr5434 and blr1087, respectively, that encode putative haloalkane dehalogenase homologues. the crude extracts of escherichia coli strains expressing mlr5434 and blr1087 showed the ability to dehalogenate 18 halogenated compounds, indicating that these orfs indeed encode haloal ... | 2005 | 16085827 |
| expression of nitrite and nitric oxide reductases in free-living and plant-associated agrobacterium tumefaciens c58 cells. | a number of the bacteria that form associations with plants are denitrifiers. to learn more about how the association with plants affects expression of denitrification genes, the regulation of nitrite and nitric oxide reductases was investigated in agrobacterium tumefaciens. analysis of free-living cells revealed that expression of the genes encoding nitrite and nitric oxide reductases, nirk and nor, respectively, requires low-oxygen conditions, nitric oxide, and the transcriptional regulator nn ... | 2005 | 16085833 |
| allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. | growth substrates containing an s-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. in the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. six different experimental results ... | 2005 | 16085834 |
| isolation and characterization of a genetically tractable photoautotrophic fe(ii)-oxidizing bacterium, rhodopseudomonas palustris strain tie-1. | we report the isolation and characterization of a phototrophic ferrous iron [fe(ii)]-oxidizing bacterium named tie-1 that differs from other fe(ii)-oxidizing phototrophs in that it is genetically tractable. under anaerobic conditions, tie-1 grows photoautotrophically with fe(ii), h2, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. tie-1 also grows chemoheterotrophically in the dark. this isolate appears to be a new strain of the purple no ... | 2005 | 16085840 |
| transcriptome-based identification of the sinorhizobium meliloti nodd1 regulon. | the nodd1 regulon of sinorhizobium meliloti was determined through the analysis of the s. meliloti transcriptome in response to the plant flavone luteolin and the overexpression of nodd1. nine new genes regulated by both nodd1 and luteolin were identified, demonstrating that nodd1 controls few functions behind nodulation in s. meliloti. | 2005 | 16085895 |
| identification of genes involved in cytochrome c biogenesis in shewanella oneidensis, using a modified mariner transposon. | a modified mariner transposon, minihimar rb1, was generated to mutagenize cells of the metal-reducing bacterium shewanella oneidensis. the use of this transposon led to the isolation of stable mutants and allowed rapid identification of disrupted genes. fifty-eight mutants, including bg104 and bg148 with transposon insertions in the cytochrome c maturation genes ccmc and ccmf1, respectively, were analyzed. both mutants were deficient in anaerobic respiration and cytochrome c production. | 2005 | 16085900 |
| evidence for a second class of s-adenosylmethionine riboswitches and other regulatory rna motifs in alpha-proteobacteria. | riboswitches are rna elements in the 5' untranslated leaders of bacterial mrnas that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. riboswitches are most common in the genomes of low gc gram-positive bacteria (for example, bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group. | 2005 | 16086852 |
| a phylogeny of bacterial rna nucleotidyltransferases: bacillus halodurans contains two trna nucleotidyltransferases. | we have analyzed the distribution of rna nucleotidyltransferases from the family that includes poly(a) polymerases (pap) and trna nucleotidyltransferases (tnt) in 43 bacterial species. genes of several bacterial species encode only one member of the nucleotidyltransferase superfamily (ntsf), and if that protein functions as a tnt, those organisms may not contain a poly(a) polymerase i like that of escherichia coli. the genomes of several of the species examined encode more than one member of the ... | 2005 | 16109934 |
| cytochrome c maturation and the physiological role of c-type cytochromes in vibrio cholerae. | vibrio cholerae lives in different habitats, varying from aquatic ecosystems to the human intestinal tract. the organism has acquired a set of electron transport pathways for aerobic and anaerobic respiration that enable adaptation to the various environmental conditions. we have inactivated the v. cholerae ccme gene, which is required for cytochrome c biogenesis. the resulting strain is deficient of all c-type cytochromes and allows us to characterize the physiological role of these proteins. u ... | 2005 | 16109941 |
| e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects. | the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ... | 2005 | 16109942 |
| identification of a new family of enzymes with potential o-acetylpeptidoglycan esterase activity in both gram-positive and gram-negative bacteria. | the metabolism of the rigid bacterial cell wall heteropolymer peptidoglycan is a dynamic process requiring continuous biosynthesis and maintenance involving the coordination of both lytic and synthetic enzymes. the o-acetylation of peptidoglycan has been proposed to provide one level of control on these activities as this modification inhibits the action of the major endogenous lytic enzymes, the lytic transglycosylases. the o-acetylation of peptidoglycan also inhibits the activity of the lysozy ... | 2005 | 16111493 |
| helicobacter hepaticus hydrogenase mutants are deficient in hydrogen-supported amino acid uptake and in causing liver lesions in a/j mice. | helicobacter hepaticus, a causative agent of chronic hepatitis and hepatocellular carcinoma in mice, expresses a nickel-containing hydrogen-oxidizing hydrogenase enzyme. growth of a hyab gene-targeted mutant was unaffected by the presence of hydrogen, unlike the wild-type strain, which showed an enhanced growth rate when supplied with h(2). hydrogenase activities in h. hepaticus were constitutive and not dependent on the inclusion of h(2) during growth. addition of nickel during growth significa ... | 2005 | 16113246 |
| compared tolerance to osmotic stress in various microorganisms: towards a survival prediction test. | the osmotic tolerance of microbial cells of different microorganisms was investigated as a function of glycerol concentration and temperatures. cells displayed specific sensitivity to dehydration in glycerol solutions. the viability of gram-negative strains (escherichia coli, bradyrhizobium japonicum), gram-positive strains (lactobacillus plantarum, l. bulgaricus), and yeasts (saccharomyces cerevisiae, candida utilis) decreased with increasing osmotic pressure. for each strain, a characteristic ... | 2005 | 16116658 |
| characterization and expression analysis of the groesl operon of bartonella bacilliformis. | the groesl operon of bartonella bacilliformis, a facultative intracellular, gram-negative bacterium and etiologic agent of oroya fever, was characterized. sequence analysis revealed an operon containing two genes of 294 (groes) and 1632 nucleotides (groel) separated by a 55-nt intergenic spacer. the operon is preceded by a 72-nt orf (orf1) that encodes a hypothetical protein with homology to a portion of the hrca repressor for groesl. a divergent fumarate hydratase c (fumc) gene lies further ups ... | 2005 | 16126349 |
| detection of homoserine lactone-like quorum sensing molecules in bradyrhizobium strains. | one hundred and forty-two bradyrhizobium strains were screened for their ability to produce n-acyl homoserine lactone-like molecules (ahls) by using an agrobacterium tumefaciens biosensor strain containing a trai-lacz fusion. approximately 22% (31 of 142) of the tested strains produced ahls that induced moderate to elevated beta-galactosidase activity levels in the biosensor strain. bradyrhizobium japonicum and bradyrhizobium elkanii strains were both shown to produce ahls. age of culture, and m ... | 2005 | 16132457 |
| structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. | comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aaob) nitrosococcus oceani and the betaproteobacterial aaob nitrosospira multiformis and nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cyca, cytochrome c(554); and cycb, cytochrome c(m)(552). the deduced protein sequen ... | 2005 | 16151127 |
| cog3926 and cog5526: a tale of two new lysozyme-like protein families. | we have identified two new lysozyme-like protein families by using a combination of sequence similarity searches, domain architecture analysis, and structural predictions. first, the p5 protein from bacteriophage phi8, which belongs to cog3926 and pfam family duf847, is predicted to have a new lysozyme-like domain. this assignment is consistent with the lytic function of p5 proteins observed in several related double-stranded rna bacteriophages. domain architecture analysis reveals two lysozyme- ... | 2005 | 16155206 |
| expression and characterization of a histidine-rich protein, hpn: potential for ni2+ storage in helicobacter pylori. | hpn is a small cytoplasmic protein found in helicobacter pylori, which binds ni2+ ions with moderate affinity. consisting of 60 amino acids, the protein is rich in histidine (28 residues, 46.7%), as well as glutamate, glycine and serine residues (in total 31.7%), and contains short repeating motifs. in the present study, we report the detailed biophysical characterization of the multimeric status and ni2+-binding properties of purified recombinant hpn under physiologically relevant conditions. t ... | 2006 | 16164421 |
| expression and characterization of a histidine-rich protein, hpn: potential for ni2+ storage in helicobacter pylori. | hpn is a small cytoplasmic protein found in helicobacter pylori, which binds ni2+ ions with moderate affinity. consisting of 60 amino acids, the protein is rich in histidine (28 residues, 46.7%), as well as glutamate, glycine and serine residues (in total 31.7%), and contains short repeating motifs. in the present study, we report the detailed biophysical characterization of the multimeric status and ni2+-binding properties of purified recombinant hpn under physiologically relevant conditions. t ... | 2006 | 16164421 |
| an iron uptake operon required for proper nodule development in the bradyrhizobium japonicum-soybean symbiosis. | rhizobia live in the soil or enter into a nitrogen-fixing symbiosis with a suitable host plant. each environment presents different challenges with respect to iron acquisition. the soybean symbiont bradyrhizobium japonicum 61a152 can utilize a variety of siderophores (fe[iii]-specific ligands). purification of iron-regulated outer membrane proteins had previously allowed the cloning of a gene, fega, from b. japonicum 61a152, whose predicted protein shares significant amino acid similarity with k ... | 2005 | 16167765 |
| diversity in domain architectures of ser/thr kinases and their homologues in prokaryotes. | ser/thr/tyr kinases (styks) commonly found in eukaryotes have been recently reported in many bacterial species. recent studies elucidating their cellular functions have established their roles in bacterial growth and development. however functions of a large number of bacterial styks still remain elusive. the organisation of domains in a large dataset of bacterial styks has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial styks. | 2005 | 16171520 |
| two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. | two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals. these systems allow cells to adapt to prevailing conditions by modifying cellular physiology, including initiating programs of gene expression, catalyzing reactions, or modifying protein-protein interactions. these signaling pathways have also been demonstrated to play a role in coordinating bact ... | 2005 | 16176121 |
| successful selection of cross-protective vaccine candidates for ornithobacterium rhinotracheale infection. | ornithobacterium rhinotracheale is a bacterial pathogen known for causing respiratory disease in poultry. in this study, we demonstrate for the first time that cross-protective immunity against different o. rhinotracheale serotypes can be induced by live vaccination. sera from these live-vaccinated and cross-protected birds were used to identify new vaccine targets by screening an o. rhinotracheale expression library. out of 20,000 screened plaques, a total of 30 cross-reactive clones were selec ... | 2005 | 16177359 |
| ethe1 mutations are specific to ethylmalonic encephalopathy. | mutations in ethe1, a gene located at chromosome 19q13, have recently been identified in patients affected by ethylmalonic encephalopathy (ee). ee is a devastating infantile metabolic disorder, characterised by widespread lesions in the brain, hyperlactic acidaemia, petechiae, orthostatic acrocyanosis, and high levels of ethylmalonic acid in body fluids. to investigate to what extent ethe1 is responsible for ee, we analysed this gene in 29 patients with typical ee and in 11 patients presenting w ... | 2006 | 16183799 |
| ethe1 mutations are specific to ethylmalonic encephalopathy. | mutations in ethe1, a gene located at chromosome 19q13, have recently been identified in patients affected by ethylmalonic encephalopathy (ee). ee is a devastating infantile metabolic disorder, characterised by widespread lesions in the brain, hyperlactic acidaemia, petechiae, orthostatic acrocyanosis, and high levels of ethylmalonic acid in body fluids. to investigate to what extent ethe1 is responsible for ee, we analysed this gene in 29 patients with typical ee and in 11 patients presenting w ... | 2006 | 16183799 |
| nh4+ currents across the peribacteroid membrane of soybean. macroscopic and microscopic properties, inhibition by mg2+, and temperature dependence indicate a subpicosiemens channel finely regulated by divalent cations. | the control of ammonium (nh(4)(+)) transport is critical in preventing futile cycles of nh(4)(+)/ammonia transport. an unusual nonselective cation channel with subpicosiemens single-channel conductance permeable to nh(4)(+) had previously been identified in the peribacteroid membrane (pbm) of symbiosomes from soybean (glycine max) nodules. here, we investigate the proposed channel mechanism and its control by luminal magnesium. currents carried by nh(4)(+) were measured in inside-out pbm patches ... | 2005 | 16183839 |
| gene products of the hupghij operon are involved in maturation of the iron-sulfur subunit of the [nife] hydrogenase from rhizobium leguminosarum bv. viciae. | in the present study, we investigate the functions of the hupghij operon in the synthesis of an active [nife] hydrogenase in the legume endosymbiont rhizobium leguminosarum bv. viciae. these genes are clustered with 14 other genes including the hydrogenase structural genes hupsl. a set of isogenic mutants with in-frame deletions (deltahupg, deltahuph, deltahupi, and deltahupj) was generated and tested for hydrogenase activity in cultures grown at different oxygen concentrations (0.2 to 2.0%) and ... | 2005 | 16199572 |
| biosynthesis of active bacillus subtilis urease in the absence of known urease accessory proteins. | bacillus subtilis contains urease structural genes but lacks the accessory genes typically required for gtp-dependent incorporation of nickel. nevertheless, b. subtilis was shown to possess a functional urease, and the recombinant enzyme conferred low levels of nickel-dependent activity to escherichia coli. additional investigations of the system lead to the suggestion that b. subtilis may use unidentified accessory proteins for in vivo urease activation. | 2005 | 16199586 |
| role of the regulatory gene rira in the transcriptional response of sinorhizobium meliloti to iron limitation. | a regulatory network of sinorhizobium meliloti genes involved in adaptation to iron-limiting conditions and the involvement of the rhizobial iron regulator gene (rira) were analyzed by mutation and microarray analyses. a constructed s. meliloti rira mutant exhibited growth defects and enhanced h2o2 sensitivity in the presence of iron, but symbiotic nitrogen fixation was not affected. to identify iron-responsive and rira-regulated s. meliloti genes, a transcriptome approach using whole-genome mic ... | 2005 | 16204511 |
| dimeric brucella abortus irr protein controls its own expression and binds haem. | brucella abortus needs to synthesize haem in order to replicate intracellularly and to produce virulence in mice. thus, to gain insight into the pathogenesis of the bacterium, regulatory proteins of the haem biosynthetic pathway were sought. an iron response regulator (irr) from bradyrhizobium japonicum, which is a close relative of brucella, was previously described as being involved in the coordination of haem biosynthesis and iron availability. the bru. abortus genome was searched for an irr ... | 2005 | 16207924 |
| the crystal structure of mismatch-specific uracil-dna glycosylase (mug) from deinococcus radiodurans reveals a novel catalytic residue and broad substrate specificity. | deinococcus radiodurans is extremely resistant to the effects of ionizing radiation. the source of the radiation resistance is not known, but an expansion of specific protein families related to stress response and damage control has been observed. dna repair enzymes are among the expanded protein families in d. radiodurans, and genes encoding five different uracil-dna glycosylases are identified in the genome. here we report the three-dimensional structure of the mismatch-specific uracil-dna gl ... | 2006 | 16223719 |
| evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in rhizobiales. | comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. however, questions about the biological significance of gene order conservation, or synteny, remain open. moreover, few comprehensive studies have been reported for rhizobial genomes. | 2005 | 16229745 |
| analysis of genetic relationship of sarothamnus scoparius microsymbionts and bradyrhizobium sp. by hybridization in microdilution wells. | dna-dna hybridization in microdilution wells was successfully used to determine the overall genomic similarity among sarothamnus scoparius microsymbionts isolated from poland and japan and representatives of bradyrhizobium species including bradyrhizobium sp. (lupinus) usda3045. geographically different s. scoparius rhizobia diverged into two genomospecies at the dna-dna similarity level of approximately 49%. polish isolates exhibited high dna similarity levels to the dna of bradyrhizobium japon ... | 2004 | 16233609 |
| atccmh, an essential component of the c-type cytochrome maturation pathway in arabidopsis mitochondria, interacts with apocytochrome c. | the maturation of c-type cytochromes requires the covalent ligation of the heme cofactor to reduced cysteines of the cxxch motif of apocytochromes. in contrast to mitochondria of other eukaryotes, plant mitochondria follow a pathway close to that found in alpha- and gamma-proteobacteria. we identified a nuclear-encoded protein, atccmh, the arabidopsis thaliana ortholog of bacterial ccmh/cycl proteins. in bacteria, ccmh and the thioredoxin ccmg are components of a periplasmic thio-reduction pathw ... | 2005 | 16236729 |
| diversification of dna sequences in the symbiotic genome of rhizobium etli. | bacteria of the genus rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. the genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. the complete nucleotide sequence of the symbiotic plasmid of rhizobium etli model strain cfn42, symbiont of the common bean plant, has been reported. to better u ... | 2005 | 16237002 |
| oligomerization of sulfolobus solfataricus signature amidase is promoted by acidic ph and high temperature. | the recombinant amidase from the hyperthermophylic archaeon sulfolobus solfataricus (ssam) a signature amidase, was cloned, purified and characterized. the enzyme is active on a large number of aliphatic and aromatic amides over the temperature range 60-95 degrees c and at ph values between 4.0 and 9.5, with an optimum at ph 5.0. the recombinant enzyme is in the form of a dimer of about 110 kd that reversibly associates into an octamer in a ph-dependent reaction. the ph dependence of the state o ... | 2005 | 16243781 |
| [effect of plant growth regulators on physiological activity of bradyrhizobium japonicum ]. | influence of plant growth regulators ivin, emistim c, eney and agrostimulin on the biomass production and exopolymers synthesis of soybean nodule bacteria, which have contrasting symbiotic properties, and glutamine synthetase activity of their cell-free extracts were studied. it was shown that the processes of the biomass and exopolymers accumulation had an opposite direction. of all preparations only ivin and agrostimulin intensificol growth activity of the microorganisms under study. the level ... | 2005 | 16250234 |
| global protein expression pattern of bradyrhizobium japonicum bacteroids: a prelude to functional proteomics. | as a prelude to using functional proteomics towards understanding the process of symbiotic nitrogen fixation between the legume soybean and the soil bacteria bradyrhizobium japonicum, we examined the total protein expression pattern of the nodule bacteria, often referred to as bacteroids. a partial proteome map was constructed by separating the total bacteroid proteins using high-resolution 2-de. of the several hundred protein spots analyzed using pmf, 180 spots were tentatively identified by se ... | 2005 | 16254929 |
| dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. | bacterial response to nitric oxide (no) is of major importance since no is an obligatory intermediate of the nitrogen cycle. transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves fnr-like transcription factors hcpr, dnr, and nnrr; two-component systems narxl and narqp; no-responsive activator norr; and nitrite-sensitive repressor nsrr. using comparative genomics approaches, we predict dna-binding motifs for these transcriptional factors and ... | 2005 | 16261196 |
| diversity of "candidatus liberibacter asiaticus," based on the omp gene sequence. | huanglongbing (yellow dragon disease) is a destructive disease of citrus. the etiological agent is a noncultured, phloem-restricted alpha-proteobacterium, "candidatus liberibacter africanus" in africa and "candidatus liberibacter asiaticus" in asia. in this study, we used an omp-based pcr-restriction fragment length polymorphism (rflp) approach to analyze the genetic variability of "ca. liberibacter asiaticus" isolates. by using five different enzymes, each the 10 isolates tested could be associ ... | 2005 | 16269671 |
| european origin of bradyrhizobium populations infecting lupins and serradella in soils of western australia and south africa. | we applied a multilocus phylogenetic approach to elucidate the origin of serradella and lupin bradyrhizobium strains that persist in soils of western australia and south africa. the selected strains belonged to different randomly amplified polymorphic dna (rapd)-pcr clusters that were distinct from rapd clusters of applied inoculant strains. phylogenetic analyses were performed with nodulation genes (noda, nodz, noll, noei), housekeeping genes (dnak, reca, glnii, atpd), and 16s-23s rrna intergen ... | 2005 | 16269740 |
| novel dna sequences from natural strains of the nitrogen-fixing symbiotic bacterium sinorhizobium meliloti. | variation in genome size and content is common among bacterial strains. identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. in this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain rm1021 of the nitrogen-fixing bacterium sinorhizobium meliloti. using strain rm1021 as the driver and the type strain ... | 2005 | 16269751 |
| three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. | soil contaminated with polychlorinated biphenyls (pcb) was used as an inoculum to grow a complex biofilm community on pcb oil (aroclor 1242) on a substratum (permanox). the biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (sscp), amplicons of the 16s rrna genes, and chemical analyses of the pcb congeners. sscp analysis of the young biofilm revealed a rather diverse microbial community with species of ... | 2005 | 16269772 |
| rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes. | rhodopseudomonas palustris, an alpha-proteobacterium, carries out three of the chemical reactions that support life on this planet: the conversion of sunlight to chemical-potential energy; the absorption of carbon dioxide, which it converts to cellular material; and the fixation of atmospheric nitrogen into ammonia. insight into the transcription-regulatory network that coordinates these processes is fundamental to understanding the biology of this versatile bacterium. with this goal in mind, we ... | 2005 | 16269786 |
| proof that burkholderia strains form effective symbioses with legumes: a study of novel mimosa-nodulating strains from south america. | twenty mimosa-nodulating bacterial strains from brazil and venezuela, together with eight reference mimosa-nodulating rhizobial strains and two other beta-rhizobial strains, were examined by amplified rrna gene restriction analysis. they fell into 16 patterns and formed a single cluster together with the known beta-rhizobia, burkholderia caribensis, burkholderia phymatum, and burkholderia tuberum. the 16s rrna gene sequences of 15 of the 20 strains were determined, and all were shown to belong t ... | 2005 | 16269788 |
| first genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to methylocapsa acidiphila b2 and for high-affinity methanotrophy involving particulate methane monooxygenase. | members of upland soil cluster alpha (usc alpha) are assumed to be methanotrophic bacteria (mb) adapted to the trace level of atmospheric methane. so far, these mb have eluded all cultivation attempts. while the 16s rrna phylogeny of usc alpha members is still not known, phylogenies constructed for the active-site polypeptide (encoded by pmoa) of particulate methane monooxygenase (pmmo) placed usc alpha next to the alphaproteobacterial methylocapsa acidiphila b2. to assess whether the pmoa tree ... | 2005 | 16269789 |
| symbiotic hydrogenase activity in bradyrhizobium sp. (vigna) increases nitrogen content in vigna unguiculata plants. | bradyrhizobium sp. (lupinus) and bradyrhizobium sp. (vigna) mutants in which hydrogenase (hup) activity was affected were constructed and analyzed. vigna unguiculata plants inoculated with the bradyrhizobium sp. (vigna) hup mutant showed reduced nitrogenase activity and also a significant decrease in nitrogen content, suggesting a relevant contribution of hydrogenase activity to plant yield. | 2005 | 16269797 |
| characterization of temporal protein production in pseudomonas aeruginosa biofilms. | phenotypic and genetic evidence supporting the notion of biofilm formation as a developmental process is growing. in the present work, we provide additional support for this hypothesis by identifying the onset of accumulation of biofilm-stage specific proteins during pseudomonas aeruginosa biofilm maturation and by tracking the abundance of these proteins in planktonic and three biofilm developmental stages. the onset of protein production was found to correlate with the progression of biofilms ... | 2005 | 16291684 |
| induction of thioredoxin is required for nodule development to reduce reactive oxygen species levels in soybean roots. | nodules are formed on legume roots as a result of signaling between symbiotic partners and in response to the activities of numerous genes. we cloned fragments of differentially expressed genes in spot-inoculated soybean (glycine max) roots. many of the induced clones were similar to known genes related to oxidative stress, such as thioredoxin and beta-carotene hydroxylase. the deduced amino acid sequences of full-length soybean cdnas for thioredoxin and beta-carotene hydroxylase were similar to ... | 2005 | 16299179 |
| four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction. | motivation: transmembrane chemoreceptors in escherichia coli utilize ligand-binding domains for detecting various external signals. the structure of this domain in the e.coli aspartate receptor, tar, is known and its signal transduction mechanism is under investigation. current domain models for this important sensory module are inaccurate and, therefore, cannot reveal the distribution of this domain within the current genomic landscape. results: we carried out sensitive and exhaustive psi-blast ... | 2005 | 16306392 |
| kinetic and thermodynamic analysis of bradyrhizobium japonicum puta-membrane associations. | in escherichia coli, proline induces tight membrane binding of the puta flavoenzyme and transforms puta from a transcriptional repressor to a membrane-associated proline catabolic enzyme. in other gram-negative bacteria such as bradyrhizobium japonicum, puta lacks dna binding activity and functions only as a proline catabolic enzyme. here, we characterize the membrane binding properties of puta from b. japonicum (bjputa) to address whether proline regulates bjputa-lipid binding similar to escher ... | 2006 | 16310755 |
| design and validation of a partial-genome microarray for transcriptional profiling of the bradyrhizobium japonicum symbiotic gene region. | the design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing bradyrhizobium japonicum is reported here. the custom-synthesized chip (affymetrix genechip) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. rna was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regr mutant and microa ... | 2006 | 16328374 |
| microarray-based detection and typing of the rhizobium nodulation gene nodc: potential of dna arrays to diagnose biological functions of interest. | environmental screening of bacteria for the presence of genes of interest is a challenging problem, due to the high variability of the nucleotide sequence of a given gene between species. here, we tackle this general issue using a particularly well-suited model system that consists of the nodulation gene nodc, which is shared by phylogenetically distant rhizobia. 41mer and 50mer oligonucleotides featuring the nucleotide diversity of two highly conserved regions of the nodc protein were spotted o ... | 2005 | 16332784 |