Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. | a quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-rflp) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. the real-time-t-rflp assay was developed by incorporating the quantitative feature of real-time pcr and the fingerprinting feature of t-rflp analysis. the assay was validated by using a model microbial community containing three pure strains, an escherich ... | 2005 | 15746346 |
| genomic analysis of bacteriophage phijl001: insights into its interaction with a sponge-associated alpha-proteobacterium. | bacteriophage phijl001 infects a novel marine bacterium in the alpha subclass of the proteobacteria isolated from the marine sponge ircinia strobilina. phijl001 is a siphovirus and forms turbid plaques on its host. the genome sequence of phijl001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. the complete genome sequence of phijl001 comprised 63,469 bp with an overall g+c content of 62%. the genome has 91 predicted ... | 2005 | 15746365 |
| lotus japonicus metabolic profiling. development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. | symbiotic nitrogen fixation (snf) in legume root nodules requires differentiation and integration of both plant and bacterial metabolism. classical approaches of biochemistry, molecular biology, and genetics have revealed many aspects of primary metabolism in legume nodules that underpin snf. functional genomics approaches, especially transcriptomics and proteomics, are beginning to provide a more holistic picture of the metabolic potential of nodules in model legumes like medicago truncatula an ... | 2005 | 15749991 |
| potential limitations of the 16s-23s rrna intergenic region for molecular detection of bartonella species. | pcr targeting the 16s-23s rrna gene intergenic transcribed spacer (its) region has been proposed as a rapid and reliable method for the detection of bartonella species dna in clinical samples. because of variation in its sequences among bartonella species, a single pcr amplification can be used to detect different species within this genus. therefore, by targeting the its region, multiple pcrs or additional sample-processing steps beyond the primary amplification can be avoided when attempting t ... | 2005 | 15750079 |
| detection of and response to signals involved in host-microbe interactions by plant-associated bacteria. | diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. this concept was first demonstrated for the members of the family rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and anima ... | 2005 | 15755957 |
| gene fusions and gene duplications: relevance to genomic annotation and functional analysis. | escherichia coli a model organism provides information for annotation of other genomes. our analysis of its genome has shown that proteins encoded by fused genes need special attention. such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. previous work overstated the number of multimodular proteins in e. coli. this work corrects ... | 2005 | 15757509 |
| bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion. | like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ... | 2005 | 15757514 |
| a novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement. | in micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. this autocrine resuscitation-promoting factor (rpf) is the founder member of a family of proteins found throughout and confined to the actinobacteria (high g + c gram-positive bacteria). the aim of this work was to search for and characterise a cognate gene family in the firmicutes (low g + c gram-positive bacteria) and obtain information about how they may ... | 2005 | 15774001 |
| transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in is element gene expression. | transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mrnas. individual mrna molecules within this population differ in the number of nucleotides they contain that are not specified by the template. when transcriptional slippage occurs in a coding sequence, translation of the resulting mrnas yields more than one protein product. except where the products of the resulting mrnas have distinct functions, transcription sl ... | 2005 | 15774026 |
| the presumptive magnetosome protein mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in magnetospirillum gryphiswaldense. | the mms16 protein has been previously found to be associated with isolated magnetosomes from two magnetospirillum strains. a function of this protein as a magnetosome-specific gtpase involved in the formation of intracellular magnetosome membrane vesicles was suggested. here we present a study of the mms16 protein from magnetospirillum gryphiswaldense to clarify its function. insertion-duplication mutagenesis of the mms16 gene did not affect the formation of magnetosome particles but resulted in ... | 2005 | 15774885 |
| invasion of lotus japonicus root hairless 1 by mesorhizobium loti involves the nodulation factor-dependent induction of root hairs. | in many legumes, including lotus japonicus and medicago truncatula, susceptible root hairs are the primary sites for the initial signal perception and physical contact between the host plant and the compatible nitrogen-fixing bacteria that leads to the initiation of root invasion and nodule organogenesis. however, diverse mechanisms of nodulation have been described in a variety of legume species that do not rely on root hairs. to clarify the significance of root hairs during the l. japonicus-me ... | 2005 | 15778455 |
| characterization of the lotus japonicus symbiotic mutant lot1 that shows a reduced nodule number and distorted trichomes. | we isolated a recessive symbiotic mutant of lotus japonicus that defines a genetic locus, lot1 (for low nodulation and trichome distortion). the nodule number per plant of the mutant was about one-fifth of that of the wild type. the lot1 mutant showed a moderate dwarf phenotype and distorted trichomes, but its root hairs showed no apparent differences to those of the wild type. infection thread formation after inoculation of mesorhizobium loti was repressed in lot1 compared to that in the wild t ... | 2005 | 15793069 |
| 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 |
| systematic association of genes to phenotypes by genome and literature mining. | one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ... | 2005 | 15799710 |
| acetylation of a fucosyl residue at the reducing end of mesorhizobium loti nod factors is not essential for nodulation of lotus japonicus. | nodml-v(c(18:1), me, cb, acfuc) is a major component of lipo-chitin oligosaccharides (lcos), or nod factors, produced by mesorhizobium loti. the presence of a 4-o-acetylated fucosyl residue (acfuc) at the reducing end has been thought to be essential for symbiotic interactions with the compatible host plant, lotus japonicus. we generated an m. loti mutant in which the noll gene is disrupted; noll has been shown to encode acetyltransferase that is responsible for acetylation of the fucosyl residu ... | 2005 | 15805124 |
| the sulfate transporter sst1 is crucial for symbiotic nitrogen fixation in lotus japonicus root nodules. | symbiotic nitrogen fixation (snf) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. little is known at the molecular level about plant transporters that mediate such exchanges. several mutants of the model legume lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. map-based cloning of ... | 2005 | 15805486 |
| completion of the genome sequence of brucella abortus and comparison to the highly similar genomes of brucella melitensis and brucella suis. | brucellosis is a worldwide disease of humans and livestock that is caused by a number of very closely related classical brucella species in the alpha-2 subdivision of the proteobacteria. we report the complete genome sequence of brucella abortus field isolate 9-941 and compare it to those of brucella suis 1330 and brucella melitensis 16 m. the genomes of these brucella species are strikingly similar, with nearly identical genetic content and gene organization. however, a number of insertion-dele ... | 2005 | 15805518 |
| biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from sphingomonas sp. strain 113p3. | oxidized polyvinyl alcohol hydrolase (oph) and polyvinyl alcohol dehydrogenase were found to be constitutively present in the periplasm of sphingomonas sp. strain 113p3 (formerly pseudomonas sp. 113p3). the oph was purified to homogeneity with a yield of 40 % and a 5.9-fold increase in specific activity. the enzyme was a homodimer consisting of 35 kda subunits. its activity was inhibited by pmsf, hg(2+) and zn(2+). the enzyme hydrolysed oxidized polyvinyl alcohol (oxidized pva) and p-nitrophenyl ... | 2005 | 15817792 |
| grafting between model legumes demonstrates roles for roots and shoots in determining nodule type and host/rhizobia specificity. | previous grafting experiments have demonstrated that legume shoots play a critical role in symbiotic development of nitrogen-fixing root nodules by regulating nodule number. here, reciprocal grafting experiments between the model legumes lotus japonicus and medicago truncatula were carried out to investigate the role of the shoot in the host-specificity of legume-rhizobia symbiosis and nodule type. lotus japonicus is nodulated by mesorhizobium loti and makes determinate nodules, whereas m. trunc ... | 2005 | 15824071 |
| peace talks and trade deals. keys to long-term harmony in legume-microbe symbioses. | 2005 | 15824283 | |
| processive lipid galactosyl/glucosyltransferases from agrobacterium tumefaciens and mesorhizobium loti display multiple specificities. | the glycosyltransferase family 21 (gt21) includes both enzymes of eukaryotic and prokaryotic organisms. many of the eukaryotic enzymes from animal, plant, and fungal origin have been characterized as uridine diphosphoglucose (udp-glc):ceramide glucosyltransferases (glucosylceramide synthases [gcs], ec 2.4.1.80). as the acceptor molecule ceramide is not present in most bacteria, the enzymatic specificities and functions of the corresponding bacterial glycosyltransferases remain elusive. in this s ... | 2005 | 15843594 |
| requirement of mgtc for brucella suis intramacrophage growth: a potential mechanism shared by salmonella enterica and mycobacterium tuberculosis for adaptation to a low-mg2+ environment. | a brucella suis mgtc mutant is defective for growth within macrophages and in low-mg(2+) medium. these phenotypes are strikingly similar to those observed with mgtc mutants from salmonella enterica and mycobacterium tuberculosis, two other pathogens that proliferate within phagosomes. mgtc appears as a remarkable virulence factor that would have been acquired by distantly related intracellular pathogens to contribute to the adaptation to a low-mg(2+) environment in the phagosome. | 2005 | 15845525 |
| microtubule dynamics in living root hairs: transient slowing by lipochitin oligosaccharide nodulation signals. | the incorporation of a fusion of green fluorescent protein and tubulin-alpha 6 from arabidopsis thaliana in root hairs of lotus japonicus has allowed us to visualize and quantify the dynamic parameters of the cortical microtubules in living root hairs. analysis of individual microtubule turnover in real time showed that only plus polymer ends contributed to overall microtubule dynamicity, exhibiting dynamic instability as the main type of microtubule behavior in lotus root hairs. comparison of t ... | 2005 | 15863517 |
| horizontal transfer of the high-pathogenicity island of yersinia pseudotuberculosis. | the horizontal transfer of genetic elements plays a major role in bacterial evolution. the high-pathogenicity island (hpi), which codes for an iron uptake system, is present and highly conserved in various enterobacteriaceae, suggesting its recent acquisition by lateral gene transfer. the aim of this work was to determine whether the hpi has kept its ability to be transmitted horizontally. we demonstrate here that the hpi is indeed transferable from a donor to a recipient yersinia pseudotubercul ... | 2005 | 15866919 |
| investigation of the catalytic triad of arylamine n-acetyltransferases: essential residues required for acetyl transfer to arylamines. | the nats (arylamine n-acetyltransferases) are a well documented family of enzymes found in both prokaryotes and eukaryotes. nats are responsible for the acetylation of a range of arylamine, arylhydrazine and hydrazine compounds. we present here an investigation into the catalytic triad of residues (cys-his-asp) and other structural features of nats using a variety of methods, including site-directed mutagenesis, x-ray crystallography and bioinformatics analysis, in order to investigate whether e ... | 2005 | 15869465 |
| genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. | bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (phx) genes and several genomic properties. there is a striking difference in the status of phx ribosomal protein (rp) genes where the archaeal genome generally encodes more rp genes and fewer phx rps compared with bacterial genomes. the increase in rps in archaea and eukaryotes compared with that in bacteria may reflect a more complex set of interactions in archaea and eukaryotes in regulating tr ... | 2005 | 15883367 |
| 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 |
| the tyra family of aromatic-pathway dehydrogenases in phylogenetic context. | the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size. | 2005 | 15888209 |
| microbial k+ channels. | 2005 | 15897296 | |
| promoter trapping in lotus japonicus reveals novel root and nodule gus expression domains. | agrobacterium-based transformation was used to introduce a promoter-less glucuronidase uida gene (beta-glucuronidase; gus) into lotus japonicus. transgenic plants were screened for gus activation at different stages after inoculation with its symbiont, mesorhizobium loti. functional gus fusion frequencies ranged from about 2 to 5% of the total number of transgenic lines. these lines provide excellent histological markers for tissue ontogeny analysis. some of the activations generated gus express ... | 2005 | 15899881 |
| identification of genomic features using microsyntenies of domains: domain teams. | the detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). our approach adopts the technique of temporarily forgetting genes and working directly with p ... | 2005 | 15899966 |
| 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 |
| nodule development induced by mesorhizobium loti mutant strains affected in polysaccharide synthesis. | the role of mesorhizobium loti surface polysaccharides on the nodulation process is not yet fully understood. in this article, we describe the nodulation phenotype of mutants affected in the synthesis of lipopolysaccharide (lps) and beta(1,2) cyclic glucan. m. loti lpsbeta2 mutant produces lps with reduced amount of o-antigen, whereas m. loti lpsbeta1 mutant produces lps totally devoid of o-antigen. both genes are clustered in the chromosome. based on amino acid sequence homology, lps sugar comp ... | 2005 | 15915643 |
| 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 |
| protein length in eukaryotic and prokaryotic proteomes. | we analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. comparing eukaryotes and prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. the magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended m ... | 2005 | 15951512 |
| 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 |
| 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 |
| seven lotus japonicus genes required for transcriptional reprogramming of the root during fungal and bacterial symbiosis. | a combined genetic and transcriptome analysis was performed to study the molecular basis of the arbuscular mycorrhiza (am) symbiosis. by testing the am phenotype of nodulation-impaired mutants and complementation analysis, we defined seven lotus japonicus common symbiosis genes (symrk, castor, pollux, sym3, sym6, sym15, and sym24) that are required for both fungal and bacterial entry into root epidermal or cortical cells. to describe the phenotype of these mutants at the molecular level, we scre ... | 2005 | 15980262 |
| codon usage comparison of novel genes in clinical isolates of haemophilus influenzae. | a similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. these analyses were performed to obtain an indication as to whether individual genes were haemophilus-like in nature, or if they probably had more recently entered the h.influenzae gene pool via horizontal gene transfer from other species. the average and sd values were calculated f ... | 2005 | 15983137 |
| 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 |
| 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 |
| 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 |
| a computational approach for identifying pathogenicity islands in prokaryotic genomes. | pathogenicity islands (pais), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (gis) that have been acquired by horizontal gene transfer event. up to now, computational approaches for identifying pais have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. these approaches often lead to the identification of genomic islands, rather than pais. | 2005 | 16033657 |
| role of trehalose transport and utilization in sinorhizobium meliloti--alfalfa interactions. | genes thua and thub in sinorhizobium meliloti rm1021 code for a major pathway for trehalose catabolism and are induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. s. meliloti strains mutated in either of these two genes were severely impaired in their ability to grow on trehalose as the sole source of carbon. thua and thub show no homology to any known enzymes in trehalose utilization. thua has similarity to proteins of unknown function in mesorhiz ... | 2005 | 16042015 |
| nodulation phenotypes of gibberellin and brassinosteroid mutants of pea. | the initiation and development of legume nodules induced by compatible rhizobium species requires a complex signal exchange involving both plant and bacterial compounds. phytohormones have been implicated in this process, although in many cases direct evidence is lacking. here, we characterize the root and nodulation phenotypes of various mutant lines of pea (pisum sativum) that display alterations in their phytohormone levels and/or perception. mutants possessing root systems deficient in gibbe ... | 2005 | 16055684 |
| 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 |
| genome wide identification of dna binding motifs of nodd-factor in sinorhizobium meliloti and mesorhizobium loti. | nodd transcription factor is a regulatory protein of nitrogen fixing bacteria, which activates expression of nod genes participating in nodulation during interaction with its symbiont legumes. it's dna binding motifs have been characterized and reported in sinorhizobium meliloti and this pattern information has been used in our theoretical analyses to detect its novel regulated genes in genomes of s. meliloti and mesorhizobium loti. m. loti, a symbiont to model legume plant lotus japonicus, show ... | 2005 | 16078361 |
| activation of olfactory-type cyclic nucleotide-gated channels is highly cooperative. | cyclic nucleotide-gated (cng) ion channels play a key role in the sensory transduction of vision and olfaction. the channels are opened by the binding of cyclic nucleotides. native olfactory cng channels are heterotetramers of cnga2, cnga4, and cngb1b subunits. upon heterologous expression, only cnga2 subunits can form functional homotetrameric channels. it is presently not known how the binding of the ligands to the four subunits is translated to channel opening. we studied activation of olfact ... | 2005 | 16081488 |
| correctly identifying the streptothricin resistance gene cassette. | 2005 | 16082007 | |
| 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 |
| 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 |
| proteins encoded by sphingomonas elodea atcc 31461 rmla and ugpg genes, involved in gellan gum biosynthesis, exhibit both dtdp- and udp-glucose pyrophosphorylase activities. | the commercial gelling agent gellan is a heteropolysaccharide produced by sphingomonas elodea atcc 31461. in this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmla) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dtdp-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan ... | 2005 | 16085866 |
| 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 |
| 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 |
| structural and dynamic properties of bacterial type iv secretion systems (review). | the type iv secretion systems (t4ss) are widely distributed among the gram-negative and -positive bacteria. these systems mediate the transfer of dna and protein substrates across the cell envelope to bacterial or eukaryotic cells generally through a process requiring direct cell-to-cell contact. bacteria have evolved t4ss for survival during establishment of pathogenic or symbiotic relationships with eukaryotic hosts. the agrobacterium tumefaciens virb/d4 t4ss and related conjugation machines s ... | 2005 | 16092524 |
| systematic targeted mutagenesis of brucella melitensis 16m reveals a major role for gntr regulators in the control of virulence. | in order to identify transcriptional regulators involved in virulence gene control in brucella melitensis, we generated a collection of 88 mutants in the arac, arsr, crp, deor, gntr, iclr, lysr, merr, rpir, and tetr families of regulators. this collection was named limur (library of mutants for regulators). we developed a method to test several mutants simultaneously in one animal in order to identify those unable to survive. this method, called the plasmid-tagged mutagenesis method, was used to ... | 2005 | 16113274 |
| comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. | whole-genome transporter analyses have been conducted on 141 organisms whose complete genome sequences are available. for each organism, the complete set of membrane transport systems was identified with predicted functions, and classified into protein families based on the transporter classification system. organisms with larger genome sizes generally possessed a relatively greater number of transport systems. in prokaryotes and unicellular eukaryotes, the significant factor in the increase in ... | 2005 | 16118665 |
| organization and metabolism of plastids and mitochondria in arbuscular mycorrhizal roots of medicago truncatula. | colonization of root cortical cells by arbuscular mycorrhizal fungi leads to marked cytological changes of plastids and mitochondria. plastids in particular are forming tubular extensions partially connecting individual organelles in a network-like way. these cytological changes correspond to an increased need for plastid and mitochondrial products during establishment and functioning of the symbiosis. the analysis of metabolite and transcript levels in mycorrhizal and nonmycorrhizal roots from ... | 2005 | 16126866 |
| comparative proteomics using 2-d gel electrophoresis and mass spectrometry as tools to dissect stimulons and regulons in bacteria with sequenced or partially sequenced genomes. | we propose two-dimensional gel electrophoresis (2-de) and mass spectrometry to define the protein components of regulons and stimulons in bacteria, including those organisms where genome sequencing is still in progress. the basic 2-de protocol allows high resolution and reproducibility and enables the direct comparison of hundreds or even thousands of proteins simultaneously. to identify proteins that comprise stimulons and regulons, peptide mass fingerprint (pmf) with matrix-assisted laser deso ... | 2005 | 16145578 |
| establishment of tn5096-based transposon mutagenesis in gordonia polyisoprenivorans. | the transposons tn5, tn10, tn611, and tn5096 were characterized regarding transposition in gordonia polyisoprenivorans strain vh2. no insertional mutants were obtained employing tn5 or tn10. the thermosensitive plasmid pcg79 harboring tn611 integrated into the chromosome of g. polyisoprenivorans; however, the insertional mutants were fairly unstable und reverted frequently to the wild-type phenotype. in contrast, various stable mutants were obtained employing tn5096-mediated transposon mutagenes ... | 2005 | 16151089 |
| biogenesis, architecture, and function of bacterial type iv secretion systems. | type iv secretion (t4s) systems are ancestrally related to bacterial conjugation machines. these systems assemble as a translocation channel, and often also as a surface filament or protein adhesin, at the envelopes of gram-negative and gram-positive bacteria. these organelles mediate the transfer of dna and protein substrates to phylogenetically diverse prokaryotic and eukaryotic target cells. many basic features of t4s are known, including structures of machine subunits, steps of machine assem ... | 2005 | 16153176 |
| 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 |
| structural characterization of a flavonoid-inducible pseudomonas aeruginosa a-band-like o antigen of rhizobium sp. strain ngr234, required for the formation of nitrogen-fixing nodules. | rhizobium (sinorhizobium) sp. strain ngr234 contains three replicons, the smallest of which (pngr234a) carries most symbiotic genes, including those required for nodulation and lipo-chito-oligosaccharide (nod factor) biosynthesis. activation of nod gene expression depends on plant-derived flavonoids, nodd transcriptional activators, and nod box promoter elements. nod boxes nb6 and nb7 delimit six different types of genes, one of which (fixf) is essential for the formation of effective nodules on ... | 2005 | 16159781 |
| 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 |
| highways of gene sharing in prokaryotes. | the extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. we have performed a rigorous phylogenetic analysis of >220,000 proteins from genomes of 144 prokaryotes to determine the contribution of gene sharing to current prokaryotic diversity, and to identify "highways" of sharing between lineages. the inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among ... | 2005 | 16176988 |
| novel pathway for arsenic detoxification in the legume symbiont sinorhizobium meliloti. | we report a novel pathway for arsenic detoxification in the legume symbiont sinorhizobium meliloti. although a majority of ars operons consist of three genes, arsr (transcriptional regulator), arsb [as(oh)3/h+ antiporter], and arsc (arsenate reductase), the s. meliloti ars operon includes an aquaglyceroporin (aqps) in place of arsb. the presence of aqps in an arsenic resistance operon is interesting, since aquaglyceroporin channels have previously been shown to adventitiously facilitate uptake o ... | 2005 | 16199569 |
| cloning and expression of ispdf from mesorhizobium loti. characterization of a bifunctional protein that catalyzes non-consecutive steps in the methylerythritol phosphate pathway. | gram-negative bacteria, plant chloroplasts, green algae and some gram-positive bacteria utilize the 2-c-methyl-d-erythritol phosphate (mep) pathway for the biosynthesis of isoprenoids. ispd, ispe, and ispf encode the enzymes required to convert mep to 2-c-methyl-d-erythritol 2,4-cyclodiphosphate (cmedp) during the biosynthesis of isopentenyl diphosphate and dimethylallyl diphosphate in the mep pathway. upon analysis of the mesorhizobium loti genome, orf mll0395 showed homology to both ispd and i ... | 2006 | 16203191 |
| 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 |
| the two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure. | the origin of the nuclear compartment has been extensively debated, leading to several alternative views on the evolution of the eukaryotic nucleus. until recently, too little phylogenetic information was available to address this issue by using multiple characters for many lineages. | 2005 | 16207356 |
| differentiation of regions with atypical oligonucleotide composition in bacterial genomes. | complete sequencing of bacterial genomes has become a common technique of present day microbiology. thereafter, data mining in the complete sequence is an essential step. new in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of orfs. we tested the usefulness of local oligonucleotide usage (ou) patterns to recognize and differentiate types of atypical oligonucleotide composition in dna sequences of ba ... | 2005 | 16225667 |
| 4-pyridoxolactonase from a symbiotic nitrogen-fixing bacterium mesorhizobium loti: cloning, expression, and characterization. | 4-pyridoxolactonase is involved in the degradation pathway for pyridoxine, a free form of vitamin b6. the gene (mlr6805) encoding the putative 4-pyridoxolactonase of nitrogen fixing symbiotic microorganism mesorhizobium loti maff303099 has been identified based on the genome database. the gene was cloned and overexpressed in a cotransformant escherichia coli cell. the recombinant enzyme was dimeric protein and contained one mole of zn2+ per mole of subunit. the enzyme showed about 30% identity w ... | 2005 | 16226926 |
| 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 |
| combining two genomes in one cell: stable cloning of the synechocystis pcc6803 genome in the bacillus subtilis 168 genome. | cloning the whole 3.5-megabase (mb) genome of the photosynthetic bacterium synechocystis pcc6803 into the 4.2-mb genome of the mesophilic bacterium bacillus subtilis 168 resulted in a 7.7-mb composite genome. we succeeded in such unprecedented large-size cloning by progressively assembling and editing contiguous dna regions that cover the entire synechocystis genome. the strain containing the two sets of genome grew only in the b. subtilis culture medium where all of the cloning procedures were ... | 2005 | 16236728 |
| 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 |
| the incp island in the genome of brucella suis 1330 was acquired by site-specific integration. | an 18,228-bp region containing open reading frames predicted to be derived from the incp plasmid or phage ancestors is present in the genomes of brucella suis biovars 1 to 4, b. canis, b. neotomae, and strains isolated from marine mammals, but not in b. melitensis, b. abortus, b. ovis, and b. suis biovar 5. the presence of circular excision intermediates and the results of an analysis of sequenced bacterial genomes suggest that the region downstream of the guaa gene is a hotspot for site-specifi ... | 2005 | 16239585 |
| a study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition. | cellular membrane lipids, of which phospholipids are the major constituents, form one of the characteristic features that distinguish archaea from other organisms. in this study, we focused on the steps in archaeal phospholipid synthetic pathways that generate polar lipids such as archaetidylserine, archaetidylglycerol, and archaetidylinositol. only archaetidylserine synthase (ass), from methanothermobacter thermautotrophicus, has been experimentally identified. other enzymes have not been fully ... | 2005 | 16243780 |
| expansion of the biocyc collection of pathway/genome databases to 160 genomes. | the biocyc database collection is a set of 160 pathway/genome databases (pgdbs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. each pgdb in the biocyc collection describes the genome and predicted metabolic network of a single organism, inferred from the metacyc database, which is a reference source on metabolic pathways from multiple organisms. in addition, each bacterial pgdb includes predicted operons for the corresponding species. the biocyc ... | 2005 | 16246909 |
| suppression of root nodule formation by artificial expression of the trenoddr1 (coat protein of white clover cryptic virus 1) gene in lotus japonicus. | trenoddr1 (trifolium repens early nodulin downregulation 1) encodes a coat protein of white clover cryptic virus 1. its expression in white clover was down-regulated at the time when root nodules formed. we surmised that its artificial expression would interfere with root nodulation. therefore, we investigated the effects of its artificial expression on the growth and root nodulation of lotus japonicus (a model legume). transformants were prepared by agrobacterium spp.-mediated transformation. t ... | 2005 | 16255246 |
| different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-r-sulfoxide reductases. | selenocysteine (sec) is found in active sites of several oxidoreductases in which this residue is essential for catalytic activity. however, many selenoproteins have fully functional orthologs, wherein cysteine (cys) occupies the position of sec. the reason why some enzymes evolve into selenoproteins if the cys versions may be sufficient is not understood. among three mammalian methionine-r-sulfoxide reductases (msrbs), msrb1 is a sec-containing protein, whereas msrb2 and msrb3 contain cys in th ... | 2005 | 16262444 |
| 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 |
| new findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea. | in order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized p(ib)-type atpases from the genomes of 188 bacteria and 22 archaea were investigated. major findings were as follows. first, a high diversity in n-terminal metal binding motifs was observed. these motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. second, the copa locus separated into two distinct p ... | 2005 | 16269744 |
| preparative synthesis of dtdp-l-rhamnose through combined enzymatic pathways. | dtdp-l-rhamnose, an important precursor of o-antigen, was prepared on a large scale from dtmp by executing an one-pot reaction in which six enzymes are involved. two enzymes, dtdp-4-keto-6-deoxy-d-glucose 3,5-epimerase and dtdp-4-keto-rhamnose reductase, responsible for the conversion of dtdp-4-keto-6-deoxy-d-glucose to dtdp-l-rhamnose, were isolated from their putative sequences in the genome of mesorhizobium loti, functionally expressed in escherichia coli, and their enzymatic activities were ... | 2006 | 16276532 |
| preferential attachment in the evolution of metabolic networks. | many biological networks show some characteristics of scale-free networks. scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. in networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. here we have investigated preferential attachment in the context of metabolic networks. | 2005 | 16281983 |
| whole-genome analyses of speciation events in pathogenic brucellae. | despite their high dna identity and a proposal to group classical brucella species as biovars of brucella melitensis, the commonly recognized brucella species can be distinguished by distinct biochemical and fatty acid characters, as well as by a marked host range (e.g., brucella suis for swine, b. melitensis for sheep and goats, and brucella abortus for cattle). here we present the genome of b. abortus 2308, the virulent prototype biovar 1 strain, and its comparison to the two other human patho ... | 2005 | 16299333 |
| 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 |
| influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. | to assess links between the diversity of nitrite-oxidizing bacteria (nob) in agricultural grassland soils and inorganic n fertilizer management, nob communities in fertilized and unfertilized soils were characterized by analysis of clone libraries and denaturing gradient gel electrophoresis (dgge) of 16s rrna gene fragments. previously uncharacterized nitrospira-like sequences were isolated from both long-term-fertilized and unfertilized soils, but dgge migration patterns indicated the presence ... | 2005 | 16332819 |
| comparative genomic analyses of the bacterial phosphotransferase system. | we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ... | 2005 | 16339738 |
| identification of lotus rhizobia by direct dna hybridization of crushed root nodules. | hybridization of crushed lotus pedunculatus root nodules with p-labeled total genomic dna probes was used to identify rhizobium loti and bradyrhizobium sp. (lotus rhizobia). probes always hybridized with homologous target dna and frequently with dnas of other strains from the same genus. intergeneric hybridization did not occur. results were comparable to those from colony hybridization. | 1987 | 16347400 |
| isolation of rhizobium loti strain-specific dna sequences by subtraction hybridization. | mixed-phase (heterogeneous) and single-phase (homogeneous) dna subtraction-hybridization methods were used to isolate specific dna probes for closely related rhizobium loti strains. in the heterogeneous method, dna from the prospective probe strain was repeatedly hybridized to a mixture of dna from cross-hybridizing strains (subtracter dna) which was immobilized on an epoxy-activated cellulose matrix. probe strain sequences which shared homology with the matrix-bound subtracter dna hybridized to ... | 1988 | 16347782 |
| single-strain versus multistrain inoculation: effect of soil mineral n availability on rhizobial strain effectiveness and competition for nodulation on chick-pea, soybean, and dry bean. | the nitrogen-fixing effectiveness of multistrain inoculants was found to be determined by both the effectiveness of the component strains and the percentage of the nodules occupied by them. multistrain formulations were always either as good as the most effective single-strain inoculant or intermediate between the most and the least effective. the percentage of nodules occupied and the amount of nitrogen fixed by the component strains of a multistrain inoculant showed highly significant linear c ... | 1990 | 16348337 |
| biotransformation of the pentahydroxy flavone quercetin by rhizobium loti and bradyrhizobium strains (lotus). | lotus rhizobia catabolized quercetin in an arabinose-based medium via a novel form of c-ring cleavage, yielding phloroglucinol and protocatechuic acid. conservation of the a and b rings of the flavone suggests that a chalcone could be formed as a transient intermediate. | 1991 | 16348495 |
| effects of ionic and osmotic strength on the glucosyltransferase of rhizobium meliloti responsible for cyclic beta-(1,2)-glucan biosynthesis. | the cyclic beta-(1,2)-glucans of rhizobium meliloti and agrobacterium tumefaciens play an important role during hypoosmotic adaptation, and the synthesis of these compounds is osmoregulated. glucosyltransferase, the enzyme responsible for cyclic beta-(1,2)-glucan biosynthesis, is present constitutively, suggesting that osmotic regulation of the biosynthesis of these glucans occurs through modulation of enzyme activity. in this study, we examined regulation of cyclic glucan biosynthesis in vitro ... | 1998 | 16349538 |
| a lithium-sensitive and sodium-tolerant 3'-phosphoadenosine-5'-phosphatase encoded by hala from the cyanobacterium arthrospira platensis is closely related to its counterparts from yeasts and plants. | 3'-phosphoadenosine-5'-phosphatase (papase) is required for the removal of toxic 3'-phosphoadenosine-5'-phosphate (pap) produced during sulfur assimilation in various eukaryotic organisms. this enzyme is a well-known target of lithium and sodium toxicity and has been used for the production of salt-resistant transgenic plants. in addition, papase has also been proposed as a target in the treatment of manic-depressive patients. one gene, hala, which could encode a protein closely related to the p ... | 2006 | 16391050 |
| identification, mutagenesis, and transcriptional analysis of the methanesulfonate transport operon of methylosulfonomonas methylovora. | recently identified genes located downstream (3') of the msmef (transport encoding) gene cluster, msmgh, and located 5' of the structural genes for methanesulfonate monooxygenase (msamo) are described from methylosulfonomonas methylovora. sequence analysis of the derived polypeptide sequences encoded by these genes revealed a high degree of identity to abc-type transporters. msme showed similarity to a putative periplasmic substrate binding protein, msmf resembled an integral membrane-associated ... | 2006 | 16391054 |
| cloning and expression of a xylitol-4-dehydrogenase gene from pantoea ananatis. | the pantoea ananatis atcc 43072 mutant strain is capable of growing with xylitol as the sole carbon source. the xylitol-4-dehydrogenase (xdh) catalyzing the oxidation of xylitol to l-xylulose was isolated from the cell extract of this strain. the n-terminal amino acid sequence of the purified protein was determined, and an oligonucleotide deduced from this peptide sequence was used to isolate the xylitol-4-dehydrogenase gene (xdh) from a p. ananatis gene library. nucleotide sequence analysis rev ... | 2006 | 16391066 |