| the cog database: an updated version includes eukaryotes. | the availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. | 2003 | 12969510 |
| characterization of a spontaneous nonmagnetic mutant of magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island. | frequent spontaneous loss of the magnetic phenotype was observed in stationary-phase cultures of the magnetotactic bacterium magnetospirillum gryphiswaldense msr-1. a nonmagnetic mutant, designated strain msr-1b, was isolated and characterized. the mutant lacked any structures resembling magnetosome crystals as well as internal membrane vesicles. the growth of strain msr-1b was impaired under all growth conditions tested, and the uptake and accumulation of iron were drastically reduced under iro ... | 2003 | 13129949 |
| complete sequence of virulence plasmid pjm1 from the marine fish pathogen vibrio anguillarum strain 775. | the virulence plasmid pjm1 enables the fish pathogen vibrio anguillarum, a gram-negative polarly flagellated comma-shaped rod bacterium, to cause a highly fatal hemorrhagic septicemic disease in salmonids and other fishes, leading to epizootics throughout the world. the pjm1 plasmid 65,009-nucleotide sequence, with an overall g+c content of 42.6%, revealed genes and open reading frames (orfs) encoding iron transporters, nonribosomal peptide enzymes, and other proteins essential for the biosynthe ... | 2003 | 13129954 |
| bradyrhizobium elkanii rtxc gene is required for expression of symbiotic phenotypes in the final step of rhizobitoxine biosynthesis. | we disrupted the rtxc gene on the chromosome of bradyrhizobium elkanii usda94 by insertion of a nonpolar aph cartridge. the rtxc mutant, designated deltartxc, produced serinol and dihydrorhizobitoxine but no rhizobitoxine, both in culture and in planta. the introduction of cosmids harboring the rtxc gene into the deltartxc mutant complemented rhizobitoxine production, suggesting that rtxc is involved in the final step of rhizobitoxine biosynthesis in b. elkanii usda94. glycine max cv. lee inocul ... | 2004 | 14711685 |
| a noncognate aminoacyl-trna synthetase that may resolve a missing link in protein evolution. | efforts to delineate the advent of many enzymes essential to protein translation are often limited by the fact that the modern genetic code evolved before divergence of the tree of life. glutaminyl-trna synthetase (glnrs) is one noteworthy exception to the universality of the translation apparatus. in eukaryotes and some bacteria, this enzyme is essential for the biosynthesis of gln-trnagln, an obligate intermediate in translation. glnrs is absent, however, in archaea, and most bacteria, organel ... | 2003 | 13679580 |
| isolation and molecular characterization of thiosulfate-oxidizing bacteria from an italian rice field soil. | in rice paddy soils an active cycling of sulfur compounds takes place. to elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. from the mpn enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. these strains were characterized by 16s rdna analyses. the isolates were affiliated to seven diffe ... | 2003 | 14529188 |
| plant recognition of symbiotic bacteria requires two lysm receptor-like kinases. | although most higher plants establish a symbiosis with arbuscular mycorrhizal fungi, symbiotic nitrogen fixation with rhizobia is a salient feature of legumes. despite this host range difference, mycorrhizal and rhizobial invasion shares a common plant-specified genetic programme controlling the early host interaction. one feature distinguishing legumes is their ability to perceive rhizobial-specific signal molecules. we describe here two lysm-type serine/threonine receptor kinase genes, nfr1 an ... | 2003 | 14534578 |
| d-xylose metabolism in hypocrea jecorina: loss of the xylitol dehydrogenase step can be partially compensated for by lad1-encoded l-arabinitol-4-dehydrogenase. | with the goal of the genetic characterization of the d-xylose pathway in hypocrea jecorina (anamorph: trichoderma reesei), we cloned the xdh1 gene, encoding nad-xylitol dehydrogenase, which catalyzes the second step of fungal d-xylose catabolism. this gene encodes a 363-amino-acid protein which has a mass of 38 kda, belongs to the zinc-containing alcohol dehydrogenase family, exhibits high sequence identity to the published sequences of xylitol dehydrogenases from yeast origins, but contains a s ... | 2003 | 14555469 |
| the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons. | is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ... | 2003 | 14563872 |
| convergent neofunctionalization by positive darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. | gene duplication is a primary source of molecular substrate for the emergence of evolutionary novelties. the chances for redundant gene sequences to evolve new functions are small compared with the probability that the copies become disabled by deleterious mutations. functional divergence after gene duplication can result in two alternative evolutionary fates: one copy acquires a novel function (neofunctionalization), or each copy adopts part of the tasks of their parental gene (subfunctionaliza ... | 2003 | 14576276 |
| one step assembly of multiple dna fragments with a designed order and orientation in bacillus subtilis plasmid. | a universal method to reconstitute sets of genes was developed. owing to the intrinsic nature of the plasmid establishment mechanism in bacillus subtilis, the assembly of five antibiotic resistance genes with a defined order and orientation was achieved. these five fragments and the plasmid have three-base protruding sequences at both ends. the protruding sequences are designed so that each fragment is ligated once in a row according to the pairing. ligation by t4 dna ligase in the presence of 1 ... | 2003 | 14576333 |
| gamma-proteobacteria aquicella lusitana gen. nov., sp. nov., and aquicella siphonis sp. nov. infect protozoa and require activated charcoal for growth in laboratory media. | several isolates, belonging to two new species of the same novel genus of gamma-proteobacteria, were recovered from drilled well (borehole) and spa water at são gemil in central portugal. these organisms are phylogenetically most closely related to the strictly intracellular uncultured species of the genus rickettsiella, which cause disease in arthropods, and to the facultatively intracellular species of the genus legionella, some of which cause legionnaires' disease and pontiac fever. the são g ... | 2003 | 14602611 |
| usefulness of rpob gene sequencing for identification of afipia and bosea species, including a strategy for choosing discriminative partial sequences. | bacteria belonging to the genera afipia and bosea are amoeba-resisting bacteria that have been recently reported to colonize hospital water supplies and are suspected of being responsible for intensive care unit-acquired pneumonia. identification of these bacteria is now based on determination of the 16s ribosomal dna sequence. however, the 16s rrna gene is not polymorphic enough to ensure discrimination of species defined by dna-dna relatedness. the complete rpob sequences of 20 strains were fi ... | 2003 | 14602635 |
| coevolution of an aminoacyl-trna synthetase with its trna substrates. | glutamyl-trna synthetases (glurss) occur in two types, the discriminating and the nondiscriminating enzymes. they differ in their choice of substrates and use either trnaglu or both trnaglu and trnagln. although most organisms encode only one glurs, a number of bacteria encode two different glurs proteins; yet, the trna specificity of these enzymes and the reason for such gene duplications are unknown. a database search revealed duplicated glurs genes in >20 bacterial species, suggesting that th ... | 2003 | 14615592 |
| the hwe histidine kinases, a new family of bacterial two-component sensor kinases with potentially diverse roles in environmental signaling. | two-component signal transduction pathways play a major role in the response of bacteria to external cues. these pathways are initiated by large collection of histidine kinases (hks) containing a sensor domain that perceives the environmental signal followed by an hk domain that triggers a histidine-aspartate phosphorelay. previous phylogenetic analyses identified 11 major families of two-component hks by comparing signature motifs within the hk domain. here we describe a new family with homolog ... | 2004 | 14702314 |
| sequence analysis of the mobile genome island pklc102 of pseudomonas aeruginosa c. | the pseudomonas aeruginosa plasmid pklc102 coexists as a plasmid and a genome island in clone c strains. whereas the related plasmid pklk106 reversibly recombines with p. aeruginosa clone k chromosomes at one of the two trna(lys) genes, pklc102 is incorporated into the trna(lys) gene only close to the pila locus. targeting of the other trna(lys) copy in the chromosome is blocked by a 23,395-bp mosaic of truncated pao open reading frames, transposons, and pklc102 homologs. annotation and phylogen ... | 2004 | 14702321 |
| an evolutionary hot spot: the pngr234b replicon of rhizobium sp. strain ngr234. | rhizobium sp. strain ngr234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. since the overall organization of the ngr234 genome is strikingly similar to that of the narrow-host-range symbiont rhizobium meliloti strain 1021 (also known as sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? study of the early symbiotic genes of both bacteria (carried by the syma plasmids) did not provide obvious answers. yet, bo ... | 2004 | 14702322 |
| the trans-acting protein interacting with the dna motif proximal to the transcriptional start site of plant l-asparaginase is bacterial sarcosine oxidase. | a trans-acting protein interacting with a specific sequence motif proximal to the transcriptional start site of the l-asparaginase promoter has been observed previously (e. vincze, j. m. reeves, e. lamping, k. j. f. farnden, and p. h. s. reynolds, plant mol. biol. 26:303-311, 1994). gel retardation experiments in which protein extracts of mesorhizobium loti and developing nodules were used suggested a bacterial origin for the repressor binding protein (rep2037). nodulation tests were performed b ... | 2004 | 14729708 |
| regulation of l-alanine dehydrogenase in rhizobium leguminosarum bv. viciae and its role in pea nodules. | alanine dehydrogenase (alda) is the principal enzyme with which pea bacteroids synthesize alanine de novo. in free-living culture, alda activity is induced by carboxylic acids (succinate, malate, and pyruvate), although the best inducer is alanine. measurement of the intracellular concentration of alanine showed that alda contributes to net alanine synthesis in laboratory cultures. divergently transcribed from alda is an asnc type regulator, aldr. mutation of aldr prevents induction of alda acti ... | 2004 | 14729712 |
| protein profile of symbiotic bacteria mesorhizobium loti maff303099 in mid-growth phase. | expressed proteins in cultured symbiotic bacteria (mesorhizobium loti maff303099) in the mid-growth phase were proteomically analyzed by two-dimensional polyacrylamide gel electrophoresis (2d-page) and capillary high-performance liquid chromatography coupled with an ion-trap mass spectrometry (ms). the genome sequence data of m. loti were used to identify the analyzed proteins. we identified 114 of the 127 proteins analyzed on 2d-page gel with some microheterogenities which were caused by post-t ... | 2003 | 14730152 |
| molecular cloning and characterization of cgt, the brucella abortus cyclic beta-1,2-glucan transporter gene, and its role in virulence. | the animal pathogen brucella abortus contains a gene cgt, which complemented sinorhizobium meliloti nodule development (ndva) and agrobacterium tumefaciens chromosomal virulence (chva) mutants. complemented strains recovered the presence of anionic cyclic beta-1,2-glucan, motility, tumor induction in a. tumefaciens, and nodule occupancy in s. meliloti, all traits strictly associated with the presence of cyclic beta-1,2-glucan in the periplasm. nucleotide sequencing revealed that b. abortus cgt c ... | 2004 | 15039351 |
| identification and characterization of genes required for biosynthesis and transport of the siderophore vibrioferrin in vibrio parahaemolyticus. | in response to low iron availability, vibrio parahaemolyticus synthesizes and secretes a polyhydroxycarboxylate-type siderophore vibrioferrin which is composed of 1 mol each of 2-ketoglutaric acid, l-alanine, ethanolamine, and citric acid. we have previously reported the cloning and characterization of the pvua gene, which encodes the 78-kda outer membrane receptor protein for ferric vibrioferrin. in this study, nine genes involved in the biosynthesis and transport of vibrioferrin have been iden ... | 2003 | 14617658 |
| degradation pathway and generation of monohydroxamic acids from the trihydroxamate siderophore deferrioxamine b. | siderophores are avid ferric ion-chelating molecules that sequester the metal for microbes. microbes elicit siderophores in numerous and different environments, but the means by which these molecules reenter the carbon and nitrogen cycles is poorly understood. the metabolism of the trihydroxamic acid siderophore deferrioxamine b by a mesorhizobium loti isolated from soil was investigated. specifically, the pathway by which the compound is cleaved into its constituent monohydroxamates was examine ... | 2004 | 14766561 |
| biochemical and proteomic analysis of the magnetosome membrane in magnetospirillum gryphiswaldense. | we analyzed the biochemical composition of the magnetosome membrane (mm) in magnetospirillum gryphiswaldense. isolated magnetosomes were associated with phospholipids and fatty acids which were similar to phospholipids and fatty acids from other subcellular compartments (i.e., outer and cytoplasmic membranes) but were present in different proportions. the binding characteristics of mm-associated proteins were studied by selective solubilization and limited proteolysis. the mm-associated proteins ... | 2004 | 14766587 |
| comparative genomics of gene-family size in closely related bacteria. | the wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. | 2004 | 15059260 |
| genomic and genetic analysis of bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes. | liu et al. recently described a group of related temperate bacteriophages that infect bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (liu et al., science 295: 2091-2094, 2002). tropism switching results from the introduction of single nucleotide substitutions at defined locations in the vr1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria ... | 2004 | 14973019 |
| a dna element recognised by the molybdenum-responsive transcription factor mode is conserved in proteobacteria, green sulphur bacteria and archaea. | the transition metal molybdenum is essential for life. escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an abc transport system. in e. coli and other proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor mode. | 2003 | 14641908 |
| purification of the formate-tetrahydrofolate ligase from methylobacterium extorquens am1 and demonstration of its requirement for methylotrophic growth. | the serine cycle methylotroph methylobacterium extorquens am1 contains two pterin-dependent pathways for c(1) transfers, the tetrahydrofolate (h(4)f) pathway and the tetrahydromethanopterin (h(4)mpt) pathway, and both are required for growth on c(1) compounds. with the exception of formate-tetrahydrofolate ligase (ftfl, alternatively termed formyl-h(4)f synthetase), all of the genes encoding the enzymes comprising these two pathways have been identified, and the corresponding gene products have ... | 2003 | 14645277 |
| new connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated rna decay system. | several prokaryotic plasmids maintain themselves in their hosts by means of diverse post-segregational cell killing systems. recent findings suggest that chromosomally encoded copies of toxins and antitoxins of post-segregational cell killing systems - such as the rele system - might function as regulatory switches under stress conditions. the rele toxin cleaves ribosome-associated transcripts, whereas another post-segregational cell killing toxin, pare, functions as a gyrase inhibitor. | 2003 | 14659018 |
| root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins. | the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ... | 2004 | 15066803 |
| identification and characterization of the ddlb, ftsq and ftsa genes upstream of ftsz in bartonella bacilliformis and bartonella henselae. | homologues of the cell division protein ftsz were previously identified in bartonella bacilliformis and bartonella henselae. we report herein that ftsz is located at the distal end of an operon that includes ddlb, ftsq, and ftsa. these genes code for homologues of d-alanine d-alanine ligase, an enzyme involved in cell wall biosynthesis, and ftsq, and ftsa, which are involved in cell division. the ddlb, ftsq, and ftsa proteins from bartonella species are most homologous to proteins in closely rel ... | 2003 | 14659047 |
| metagenome survey of biofilms in drinking-water networks. | most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. first, a sequence analysis of 650 16s rrna clones indicated a high diversity within the biofilm communities, with the ma ... | 2003 | 14660379 |
| trans-editing of mischarged trnas. | aminoacyl-trna synthetases (aarss) are multidomain proteins that specifically attach amino acids to their cognate trnas. their most conserved, and presumably evolutionarily oldest, domains are the catalytic cores, which activate amino acids and transfer them to the 3' ends of trnas. additional domains appended to or inserted in the body of aarss increase efficiency and specificity of the aminoacylation process, either by providing additional trna contacts, or by hydrolyzing noncognate amino acid ... | 2003 | 14663147 |
| microorganisms resistant to free-living amoebae. | free-living amoebae feed on bacteria, fungi, and algae. however, some microorganisms have evolved to become resistant to these protists. these amoeba-resistant microorganisms include established pathogens, such as cryptococcus neoformans, legionella spp., chlamydophila pneumoniae, mycobacterium avium, listeria monocytogenes, pseudomonas aeruginosa, and francisella tularensis, and emerging pathogens, such as bosea spp., simkania negevensis, parachlamydia acanthamoebae, and legionella-like amoebal ... | 2004 | 15084508 |
| quorum sensing in nitrogen-fixing rhizobia. | members of the rhizobia are distinguished for their ability to establish a nitrogen-fixing symbiosis with leguminous plants. while many details of this relationship remain a mystery, much effort has gone into elucidating the mechanisms governing bacterium-host recognition and the events leading to symbiosis. several signal molecules, including plant-produced flavonoids and bacterially produced nodulation factors and exopolysaccharides, are known to function in the molecular conversation between ... | 2003 | 14665677 |
| mechanistic diversity of fosfomycin resistance in pathogenic microorganisms. | microbial resistance to the antibiotic fosfomycin [(1r,2s)-epoxypropylphosphonic acid, 1] is known to be mediated by thiol transferase enzymes fosa and fosb, which catalyze the addition of glutathione and l-cysteine to c1 of the oxirane, respectively. a probe of the microbial genome database reveals a related group of enzymes (fosx). the genes mlr3345 from mesorhizobium loti and lmo1702 from listeria monocytogenes were cloned and the proteins expressed. this heretofore unrecognized group of enzy ... | 2003 | 14677948 |
| null mutation of hvra compensates for loss of an essential rela/spot-like gene in rhodobacter capsulatus. | we report that a single rela/spot-like gene exists on the rhodobacter capsulatus chromosome, and its mutational loss is lethal. this gene could be mutated only under a mutational background of a null mutation in the nucleoid protein hvra. this result suggests that there may be a direct link between hvra-regulated promoters and the ppgpp-related stringent response. | 2004 | 14679243 |
| cloning and characterization of the gene encoding the major cell-associated phospholipase a of legionella pneumophila, plab, exhibiting hemolytic activity. | legionella pneumophila, the causative agent of legionnaires' disease, is an intracellular pathogen of amoebae, macrophages, and epithelial cells. the pathology of legionella infections involves alveolar cell destruction, and several proteins of l. pneumophila are known to contribute to this ability. by screening a genomic library of l. pneumophila, we found an additional l. pneumophila gene, plab, which coded for a hemolytic activity and contained a lipase consensus motif in its deduced protein ... | 2004 | 15102773 |
| comparison of the 1.85 a structure of cyp154a1 from streptomyces coelicolor a3(2) with the closely related cyp154c1 and cyps from antibiotic biosynthetic pathways. | the genus streptomyces produces two-thirds of microbially derived antibiotics. polyketides form the largest and most diverse group of these natural products. antibiotic diversity of polyketides is generated during their biosynthesis by several means, including postpolyketide modification performed by oxidoreductases, a broad group of enzymes including cytochrome p450 monooxygenases (cyps). cyps catalyze site-specific oxidation of macrolide antibiotic precursors significantly affecting antibiotic ... | 2004 | 14691240 |
| evidence for a symbiosis island involved in horizontal acquisition of pederin biosynthetic capabilities by the bacterial symbiont of paederus fuscipes beetles. | pederin belongs to a group of antitumor compounds found in terrestrial beetles and marine sponges. it is used by apparently all members of the rove beetle genera paederus and paederidus as a chemical defense against predators. however, a recent analysis of the putative pederin biosynthesis (ped) gene cluster strongly suggests that pederin is produced by bacterial symbionts. we have sequenced an extended region of the symbiont genome to gain further insight into the biology of this as-yet-uncultu ... | 2004 | 14973122 |
| h protein of bacteriophage 16-3 and rkpm protein of sinorhizobium meliloti 41 are involved in phage adsorption. | the strain-specific capsular polysaccharide kr5 antigen of sinorhizobium meliloti 41 is required both for invasion of the symbiotic nodule and for the adsorption of bacteriophage 16-3. in order to know more about the genes involved in these events, bacterial mutants carrying an altered phage receptor were identified by using host range phage mutants. a representative mutation was localized in the rkpm gene by complementation and dna sequence analysis. a host range phage mutant isolated on these ... | 2004 | 14996788 |
| the nitrogen-fixing symbiotic bacterium mesorhizobium loti has and expresses the gene encoding pyridoxine 4-oxidase involved in the degradation of vitamin b6. | the gene product of mll6785 of a nitrogen-fixing symbiotic bacterium mesorhizobium loti maff303099 was identified as pyridoxine 4-oxidase, the first enzyme in the vitamin b6-degradation pathway. the gene was cloned and ligated into pet-21a+. escherichia coli bl21(de3) was co-transformed with the constructed plasmid plus pky206 containing groesl genes encoding chaperonins. the overexpressed protein was purified to homogeneity by the ammonium sulfate fractionation and three chromatography steps. t ... | 2004 | 15135526 |
| regulatory role of rhizobium etli cnpaf512 fnrn during symbiosis. | the rhizobium etli cnpaf512 fnrn gene was identified in the fixabcx rpon(2) region. the corresponding protein contains the hallmark residues characteristic of proteins belonging to the class ib group of fnr-related proteins. the expression of r. etli fnrn is highly induced under free-living microaerobic conditions and during symbiosis. this microaerobic and symbiotic induction of fnrn is not controlled by the sigma factor rpon and the symbiotic regulator nifa or fixlj, but it is due to positive ... | 2004 | 15006745 |
| characteristics of a new enantioselective thermostable dipeptidase from brevibacillus borstelensis bcs-1 and its application to synthesis of a d-amino-acid-containing dipeptide. | a new thermostable dipeptidase gene was cloned from the thermophile brevibacillus borstelensis bcs-1 by genetic complementation of the d-glu auxotroph escherichia coli wm335 on a plate containing d-ala-d-glu. nucleotide sequence analysis revealed that the gene included an open reading frame coding for a 307-amino-acid sequence with an m(r) of 35,000. the deduced amino acid sequence of the dipeptidase exhibited 52% similarity with the dipeptidase from listeria monocytogenes. the enzyme was purifi ... | 2004 | 15006780 |
| the sinorhizobium meliloti fur gene regulates, with dependence on mn(ii), transcription of the sitabcd operon, encoding a metal-type transporter. | sinorhizobium meliloti is an alpha-proteobacterium able to induce nitrogen-fixing nodules on roots of specific legumes. in order to propagate in the soil and for successful symbiotic interaction the bacterium needs to sequester metals like iron and manganese from its environment. the metal uptake has to be in turn tightly regulated to avoid toxic effects. in this report we describe the characterization of a chromosomal region of s. meliloti encoding the sitabcd operon and the putative regulatory ... | 2004 | 15150249 |
| diverse organization of genes of the beta-ketoadipate pathway in members of the marine roseobacter lineage. | members of the roseobacter lineage, an ecologically important marine clade within the class alpha-proteobacteria, harbor genes for the protocatechuate branch of the beta-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. the genes of this pathway are typically clustered, although gene order varies among organisms. here we characterize genes linked to pcah and -g, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the roseobacter lin ... | 2004 | 15006791 |
| phylogenomics of the reproductive parasite wolbachia pipientis wmel: a streamlined genome overrun by mobile genetic elements. | the complete sequence of the 1,267,782 bp genome of wolbachia pipientis wmel, an obligate intracellular bacteria of drosophila melanogaster, has been determined. wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. analysis of the wmel genome, in particular phylogenomic comparisons with other intracellular bacteria, has reveale ... | 2004 | 15024419 |
| characteristic biological activities of lipopolysaccharides from sinorhizobium and mesorhizobium. | the biological actions of lipopolysaccharides (lpss) from sinorhizobium meliloti, mesorhizobium loti and escherichia coli were compared. in biological activities including lethality, production of tumor necrosis factor (tnf)-alpha and nitric oxide (no), adjuvant action and limulus activity, lps from s. meliloti exhibited stronger actions than lps from m. loti, but had a weaker action than lps from e. coli. on the other hand, m. loti lps showed a higher activity to activate human complement than ... | 2004 | 15025821 |
| infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes. | bacteria belonging to the genera rhizobium, mesorhizobium, sinorhizobium, bradyrhizobium, and azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. the interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that aris ... | 2004 | 15187185 |
| phenotypic and genotypic analysis of rhizobia isolated from pasture legumes native of sardinia and asinara island. | thirty-five rhizobial strains were isolated from nodules of lotus edulis, l. ornithopodioides, l. cytisoides, hedysarum coronarium, ornithopus compressus and scorpiurus muricatus growing in sardinia and asinara island. basic characteristics applied to identification of rhizobia such as symbiotic properties, antibiotic- and salt-resistance, temperate-sensitivities, utilization of different sources of carbon and nitrogen were studied. the results from the 74 metabolic tests were used for cluster a ... | 2004 | 15031655 |
| mutational analysis and biochemical characterization of the burkholderia thailandensis dw503 quorum-sensing network. | numerous gram-negative bacteria communicate and regulate gene expression through a cell density-responsive mechanism termed quorum sensing (qs), which involves the synthesis and perception of diffusible n-acyl-homoserine lactones (ahl). in this study we genetically and physiologically characterized the burkholderia thailandensis dw503 qs network. in silico analysis of the b. thailandensis genome revealed the presence of at least three ahl synthases (ahs) and five transcriptional regulators belon ... | 2004 | 15205437 |
| the louse-borne human pathogen bartonella quintana is a genomic derivative of the zoonotic agent bartonella henselae. | we present the complete genomes of two human pathogens, bartonella quintana (1,581,384 bp) and bartonella henselae (1,931,047 bp). the two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. a primary difference between the two pathogens is their reservoir ecology. whereas b. quintana is a specialist, using ... | 2004 | 15210978 |
| enzymatic synthesis of lipid a molecules with four amide-linked acyl chains. lpxa acyltransferases selective for an analog of udp-n-acetylglucosamine in which an amine replaces the 3"-hydroxyl group. | lpxa of escherichia coli catalyzes the acylation of the glucosamine 3-oh group of udp-glcnac, using r-3-hydroxymyristoyl-acyl carrier protein (acp) as the donor substrate. we now demonstrate that lpxa in cell extracts of mesorhizobium loti and leptospira interrogans, which synthesize lipid a molecules containing 2,3-diamino-2,3-dideoxy-d-glucopyranose (glcn3n) units in place of glucosamine, do not acylate udp-glcnac. instead, these lpxa acyltransferases require a udp-glc-nac derivative (designat ... | 2004 | 15044493 |
| characterization of nopp, a type iii secreted effector of rhizobium sp. strain ngr234. | the type three secretion system (ttss) encoded by pngr234a, the symbiotic plasmid of rhizobium sp. strain ngr234, is responsible for the flavonoid- and nodd1-dependent secretion of nodulation outer proteins (nops). abolition of secretion of all or specific nops significantly alters the nodulation ability of ngr234 on many of its hosts. in the closely related strain rhizobium fredii usda257, inactivation of the ttss modifies the host range of the mutant so that it includes the improved glycine ma ... | 2004 | 15231809 |
| oxidation and transamination of the 3"-position of udp-n-acetylglucosamine by enzymes from acidithiobacillus ferrooxidans. role in the formation of lipid a molecules with four amide-linked acyl chains. | lipid a, a major component of the outer membranes of escherichia coli and other gram-negative bacteria, is usually constructed around a beta-1',6-linked glucosamine disaccharide backbone. however, in organisms like acidithiobacillus ferrooxidans, leptospira interrogans, mesorhizobium loti, and legionella pneumophila, one or both glucosamine residues are replaced with the sugar 2,3-diamino-2,3-dideoxy-d-glucopyranose. we now report the identification of two proteins, designated gnna and gnnb, inv ... | 2004 | 15044494 |
| molecular analysis of carbon monoxide-oxidizing bacteria associated with recent hawaiian volcanic deposits. | genomic dna extracts from four sites at kilauea volcano were used as templates for pcr amplification of the large subunit (coxl) of aerobic carbon monoxide dehydrogenase. the sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. pcr primers amplified coxl sequences from the omp clade of co oxidizers, which includes isolates such as oligotropha carboxidovorans, mycobacterium tuber ... | 2004 | 15240307 |
| cheese whey: an alternative growth and protective medium for rhizobium loti cells. | cheese whey (cw)-based growth medium efficiently protects rhizobium loti cells during freezing and desiccation and can maintain their growth in a manner similar to that of traditional mannitol-based medium (yem). the cheese-whey-based medium (cw) improved viability when used to re-suspend cell pellets kept at -20 degrees c and -80 degrees c and resulted in the survival of over 90% of the cells. moreover, bacterial pellets obtained from cells grown in cw withstand desiccation better than cells gr ... | 2004 | 15052419 |
| a new amidohydrolase from bordetella or alcaligenes strain fb188 with similarities to histone deacetylases. | the full-length gene encoding the histone deacetylase (hdac)-like amidohydrolase (hdah) from bordetella or alcaligenes (bordetella/alcaligenes) strain fb188 (dsm 11172) was cloned using degenerate primer pcr combined with inverse-pcr techniques and ultimately expressed in escherichia coli. the expressed enzyme was biochemically characterized and found to be similar to the native enzyme for all properties examined. nucleotide sequence analysis revealed an open reading frame of 1,110 bp which enco ... | 2004 | 15060035 |
| expression islands clustered on the symbiosis island of the mesorhizobium loti genome. | rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. the establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. we developed a macroarray for mesorhizobium loti maff303099, a microsymbiont of the model legume lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. global transcriptional ... | 2004 | 15060047 |
| where does bacterial replication start? rules for predicting the oric region. | three methods, based on dna asymmetry, the distribution of dnaa boxes and dnaa gene location, were applied to identify the putative replication origins in 120 chromosomes. the chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. dna asymmetry is the most universal method of putative oric identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. the three meth ... | 2004 | 15258248 |
| transcriptional profiling of caulobacter crescentus during growth on complex and minimal media. | microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (pye) and minimal salts medium with glucose or xylose as the carbon source. nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. the differentially expressed genes included many encoding transport systems, most notably di ... | 2004 | 14973021 |
| comparative whole-genome hybridization reveals genomic islands in brucella species. | brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and malta fever in humans. based on host preference, the genus is divided into six species. brucella abortus, b. melitensis, and b. suis are pathogenic to humans, whereas b. ovis and b. neotomae are nonpathogenic to humans and b. canis human infections are rare. limited genome diversity exists among brucella species. comparison of brucella species whole genomes is, therefore, likel ... | 2004 | 15262941 |
| unraveling the function of the rhodospirillum rubrum activator of polyhydroxybutyrate (phb) degradation: the activator is a phb-granule-bound protein (phasin). | efficient hydrolysis of native poly(3-hydroxybutyrate) (nphb) granules in vitro by soluble phb depolymerase of rhodospirillum rubrum requires pretreatment of nphb with an activator compound present in r. rubrum cells (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). edman sequencing of the purified activator (17.4 kda; matrix-assisted laser desorption ionization-time of flight mass spectrometry) revealed identity to a hypothetical protein deduced from a partially sequenced r. rubru ... | 2004 | 15060050 |
| yapi, a new yersinia pseudotuberculosis pathogenicity island. | pathogenicity islands (pais) are chromosomal clusters of pathogen-specific virulence genes often found at trna loci. in the yersinia pseudotuberculosis 32777 chromosome, we characterized a 98-kb segment that has all of the characteristic features of a pai, including insertion in a (phenylalanine) trna gene, the presence of a bacteriophage-like integrase-encoding gene, and direct repeats at the integration sites. the g+c content of the segment ranges from 31 to 60%, reflecting a genetic mosaic: t ... | 2004 | 15271940 |
| fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy. | a small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic dna (i.e. mm and m long, respectively) in a highly organized fashion. to understand how such genomic architecture could be achieved, escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly com ... | 2004 | 15060178 |
| excision of the shigella resistance locus pathogenicity island in shigella flexneri is stimulated by a member of a new subgroup of recombination directionality factors. | pathogenicity islands are capable of excision and insertion within bacterial chromosomes. we describe a protein, rox, that stimulates excision of the shigella resistance locus pathogenicity island in shigella flexneri. sequence analysis suggests that rox belongs to a new subfamily of recombination directionality factors, which includes proteins from p4, enterohemorrhagic escherichia coli, and yersinia pestis. | 2004 | 15292162 |
| urease-encoding genes in ammonia-oxidizing bacteria. | many but not all ammonia-oxidizing bacteria (aob) produce urease (urea amidohydrolase, ec 3.5.1.5) and are capable of using urea for chemolithotrophic growth. we sequenced the urease operons from two aob, the beta-proteobacterium nitrosospira sp. strain npav and the gamma-proteobacterium nitrosococcus oceani. in both organisms, all seven urease genes were contiguous: the three structural urease genes ureabc were preceded and succeeded by the accessory genes ured and ureefg, respectively. green f ... | 2004 | 15066830 |
| omega-amino acid:pyruvate transaminase from alcaligenes denitrificans y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines. | alcaligenes denitrificans y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (apta) was cloned. the gene was functionally expressed in escherichia coli bl21 by using an isopropyl-beta-d-thiogalactopyranoside (iptg)-inducible pet expression system (9.6 u/mg), and the recombinant apta was purified to show a specific a ... | 2004 | 15066855 |
| characterization of three functional high-affinity ammonium transporters in lotus japonicus with differential transcriptional regulation and spatial expression. | ammonium is a primary source of nitrogen for plants. in legume plants ammonium can also be obtained by symbiotic nitrogen fixation, and nh(4)(+) is also a regulator of early and late symbiotic interaction steps. ammonium transporters are likely to play important roles in the control of nodule formation as well as in nitrogen assimilation. two new genes, ljamt1;2 and ljamt1;3, were cloned from lotus japonicus. both were able to complement the growth defect of a yeast (saccharomyces cerevisiae) am ... | 2004 | 15075393 |
| identification of pimr as a positive regulator of pimaricin biosynthesis in streptomyces natalensis. | sequencing of the dna region on the left fringe of the pimaricin gene cluster revealed the presence of a 3.6-kb gene, pimr, whose deduced product (1,198 amino acid residues) was found to have amino acid sequence homology with bacterial regulatory proteins. database comparisons revealed that pimr represents the archetype of a new class of regulators, combining a streptomyces antibiotic regulatory protein (sarp)-like n-terminal section with a c-terminal half homologous to guanylate cyclases and la ... | 2004 | 15090496 |
| different patterns of evolution for duplicated dna repair genes in bacteria of the xanthomonadales group. | dna repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. the importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes. | 2004 | 15333143 |
| the pgaabcd locus of escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. | production of a polysaccharide matrix is a hallmark of bacterial biofilms, but the composition of matrix polysaccharides and their functions are not widely understood. previous studies of the regulation of escherichia coli biofilm formation suggested the involvement of an unknown adhesin. we now establish that the pgaabcd (formerly ycdsrqp) locus affects biofilm development by promoting abiotic surface binding and intercellular adhesion. all of the pga genes are required for optimal biofilm form ... | 2004 | 15090514 |
| new rna motifs suggest an expanded scope for riboswitches in bacterial genetic control. | the expression of certain genes involved in fundamental metabolism is regulated by metabolite-binding "riboswitch" elements embedded within their corresponding mrnas. we have identified at least six additional elements within the bacillus subtilis genome that exhibit characteristics of riboswitch function (glms, gcvt, ydao/yuaa, ykkc/yxkd, ykok, and yybp/ykoy). these motifs exhibit extensive sequence and secondary-structure conservation among many bacterial species and occur upstream of related ... | 2004 | 15096624 |
| in search of rnase p rna from microbial genomes. | a simple procedure has been developed to quickly retrieve and validate the dna sequence encoding the rna subunit of ribonuclease p (rnase p rna) from microbial genomes. rnase p rna sequences were identified from 94% of bacterial and archaeal complete genomes where previously no rnase p rna was annotated. a sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative rnase p rna in terms of conserved primary features an ... | 2004 | 15337843 |
| occurrence and potential diagnostic applications of serological cross-reactivities between brucella and other alpha-proteobacteria. | agrobacterium, sinorhizobium, and ochrobactrum are genera closely related to brucella but, in contrast to the latter, are not pathogenic for humans and animals. we studied by an indirect enzyme-linked immunosorbent assay (elisa) the reactivities of brucellosis sera against cytosolic (cyt) and membrane (ma) antigens from these nonpathogenic bacteria, and we evaluated the potential usefulness of these cross-reactions for the diagnosis of brucellosis in humans, sheep, cows, and dogs. canine infecti ... | 2004 | 15358645 |
| genome-wide molecular clock and horizontal gene transfer in bacterial evolution. | we describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. the approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straig ... | 2004 | 15375139 |
| teir, a luxr-type transcription factor required for testosterone degradation in comamonas testosteroni. | we have identified a new steroid-inducible gene (designated teir [testosterone-inducible regulator]) in comamonas testosteroni that is required for testosterone degradation. nucleotide sequence analysis of teir predicts a 391-amino-acid protein which shows homology between residues 327 and 380 (c-terminal domain) to the luxr helix-turn-helix dna binding domain and between residues 192 and 227 to the pas sensor domain. this domain distribution resembles that described for trar, a specific transcr ... | 2004 | 14973025 |
| release of periplasmic proteins of brucella suis upon acidic shock involves the outer membrane protein omp25. | the survival and replication of brucella in macrophages is initially triggered by a low intraphagosomal ph. in order to identify proteins released by brucella during this early acidification step, we analyzed brucella suis conditioned medium at various ph levels. no significant proteins were released at ph 4.0 in minimal medium or citrate buffer, whereas in acetate buffer, b. suis released a substantial amount of soluble proteins. comparison of 13 n-terminal amino acid sequences determined by ed ... | 2004 | 15385468 |
| the ton system, an abc transporter, and a universally conserved gtpase are involved in iron utilization by brucella melitensis 16m. | brucella spp. are gram-negative intracellular facultative pathogens that are known to produce 2,3-dihydroxybenzoic acid (dhba), a catechol siderophore that is essential for full virulence in the natural host. the mechanism of dhba entry into brucella and other gram-negative bacteria is poorly understood. using mini-tn5kmcat mutagenesis, we created a transposon library of brucella melitensis 16m and isolated 32 mutants with a defect in iron acquisition or assimilation. three of these transposon m ... | 2004 | 15385478 |
| comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from methylocystis strain sc2. | in addition to the conventional pmoa gene (pmoa1) encoding the active site polypeptide of particulate methane monooxygenase, a novel pmoa gene copy (pmoa2) is widely distributed among type ii methanotrophs (methane-oxidizing bacteria [mob]) (m. tchawa yimga, p. f. dunfield, p. ricke, j. heyer, and w. liesack, appl. environ. microbiol. 69:5593-5602, 2003). here we report that the pmoa1 and pmoa2 gene copies in the type ii mob methylocystis strain sc2 are each part of a complete pmocab gene cluste ... | 2004 | 15128567 |
| genome-wide comparison of the his-to-asp phosphorelay signaling components of three symbiotic genera of rhizobia. | histidine-to-aspartate (his-asp) phosphorelay (or two-component) systems are very common signal transduction mechanisms that are implicated in a wide variety of cellular responses to environmental stimuli. the his-asp phosphorelay components include "sensor histidine kinase (hk)", "phosphotransfer intermediate (hpt)", and "response regulator (rr)". with special reference to three bacterial species (mesorhizobium loti, bradyrhizobium japonicum, sinorhizobium meliloti), each of which belongs to a ... | 2004 | 15141946 |
| expression profiling in medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program. | in this study, we describe a large-scale expression-profiling approach to identify genes differentially regulated during the symbiotic interaction between the model legume medicago truncatula and the nitrogen-fixing bacterium sinorhizobium meliloti. macro- and microarrays containing about 6,000 probes were generated on the basis of three cdna libraries dedicated to the study of root symbiotic interactions. the experiments performed on wild-type and symbiotic mutant material led us to identify a ... | 2004 | 15466239 |
| bacterial signal transduction network in a genomic perspective. | bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. the complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. comparative studies revealed certain general trends in the organization of diverse signalling systems. these include (i) modular structure of signalling proteins; (ii) comm ... | 2004 | 15142243 |
| characterization of the icmh and icmf genes required for legionella pneumophila intracellular growth, genes that are present in many bacteria associated with eukaryotic cells. | legionella pneumophila, the causative agent of legionnaires' disease, replicates intracellularly within a specialized phagosome of mammalian and protozoan host cells, and the icm/dot type iv secretion system has been shown to be essential for this process. unlike all the other known icm/dot proteins, the icmf protein, which was described before, and the icmh protein, which is characterized here, have homologous proteins in many bacteria (such as yersinia pestis, salmonella enterica, rhizobium le ... | 2004 | 15155646 |
| inactivation of the flagellin gene flaa in magnetospirillum gryphiswaldense results in nonmagnetotactic mutants lacking flagellar filaments. | magnetotactic bacteria synthesize magnetosomes, which cause them to orient and migrate along magnetic field lines. the analysis of magnetotaxis and magnetosome biomineralization at the molecular level has been hindered by the unavailability of genetic methods, namely the lack of a means to introduce directed gene-specific mutations. here we report a method for knockout mutagenesis by homologous recombination in magnetospirillum gryphiswaldense. multiple flagellin genes, which are unlinked in the ... | 2004 | 15184166 |
| comparative genomics of the ftsk-hera superfamily of pumping atpases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. | recently, it has been shown that a predicted p-loop atpase (the hera or mlaa protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the trwb atpase. in this study, the ftsk-hera superfamily of p-loop atpases, in which the hera clade comprises one of the major branches, is analyzed in detail. we show that, in addition to the ftsk and hera clades, this ... | 2004 | 15466593 |
| regb/rega, a highly conserved redox-responding global two-component regulatory system. | the reg regulon from rhodobacter capsulatus and rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. the redox signal that is detected by the membrane-bound sensor kinase, regb, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c o ... | 2004 | 15187184 |
| transgenic lotus japonicus with an ethylene receptor gene cm-ers1/h70a enhances formation of infection threads and nodule primordia. | ethylene inhibits the establishment of symbiosis between rhizobia and legumes. to examine how and when endogenous ethylene inhibits rhizobial infection and nodulation, we produced transgenic lotus japonicus carrying the mutated melon ethylene receptor gene cm-ers1/h70a that confers ethylene insensitivity and fixes the transgene in the t(3) generation. the resultant transgenic plants showed reduced ethylene sensitivity because of 1-aminocyclopropane-1-carboxylate resistance and increased flowerin ... | 2004 | 15111717 |
| patterns of bacterial gene movement. | lateral gene transfer has emerged as an important force in bacterial evolution. a substantial number of genes can be inserted into or deleted from genomes through the process of lateral transfer. in this study, we looked for atypical occurrence of genes among related organisms to detect laterally transferred genes. we have analyzed 50 bacterial complete genomes from nine groups. for each group we use a 16s rrna phylogeny and a comparison of protein similarity to map gene insertions/deletions ont ... | 2004 | 15115802 |
| sinorhizobium meliloti sulfotransferase that modifies lipopolysaccharide. | sinorhizobium meliloti is a gram-negative soil bacterium found either in free-living form or as a nitrogen-fixing endosymbiont of a plant structure called the nodule. symbiosis between s. meliloti and its plant host alfalfa is dependent on bacterial transcription of nod genes, which encode the enzymes responsible for synthesis of nod factor. s. meliloti nod factor is a lipochitooligosaccharide that undergoes a sulfate modification essential for its biological activity. sulfate also modifies the ... | 2004 | 15205418 |
| two c-p lyase operons in pseudomonas stutzeri and their roles in the oxidation of phosphonates, phosphite, and hypophosphite. | dna sequencing and analysis of two distinct c-p lyase operons in pseudomonas stutzeri wm88 were completed. the htxabcdefghijklmn operon encodes a hypophosphite-2-oxoglutarate dioxygenase (htxa), whereas the predicted amino acid sequences of htxb to htxn are each homologous to the components of the escherichia coli phn operon, which encodes c-p lyase, although homologs of e. coli phnf and phno are absent. the genes in the htx operon are cotranscribed based on gene organization, and the presence o ... | 2004 | 15231805 |
| properties of a novel thermostable glucoamylase from the hyperthermophilic archaeon sulfolobus solfataricus in relation to starch processing. | a gene (ssg) encoding a putative glucoamylase in a hyperthermophilic archaeon, sulfolobus solfataricus, was cloned and expressed in escherichia coli, and the properties of the recombinant protein were examined in relation to the glucose production process. the recombinant glucoamylase was extremely thermostable, with an optimal temperature at 90 degrees c. the enzyme was most active in the ph range from 5.5 to 6.0. the enzyme liberated beta-d-glucose from the substrate maltotriose, and the subst ... | 2004 | 15240266 |
| fur is involved in manganese-dependent regulation of mnta (sita) expression in sinorhizobium meliloti. | fur is a transcriptional regulator involved in iron-dependent control of gene expression in many bacteria. in this work we analyzed the phenotype of a fur mutant in sinorhizobium meliloti, an alpha-proteobacterium that fixes n(2) in association with host plants. we demonstrated that some functions involved in high-affinity iron transport, siderophore production, and iron-regulated outer membrane protein expression respond to iron in a fur-independent manner. however, manganese-dependent expressi ... | 2004 | 15240318 |
| lotus japonicus ljkup is induced late during nodule development and encodes a potassium transporter of the plasma membrane. | the kup family of potassium transporters in plants is large but poorly characterized. we isolated and characterized the first kup transporter from a legume, ljkup of lotus japonicus. although expressed throughout plants, ljkup transcript levels were highest in nodules. induction of ljkup expression occurred late during nodule development, at a time of rapid organ expansion. a high level of ljkup expression was maintained in mature, full-sized nodules. however, induction of ljkup expression was i ... | 2004 | 15242173 |
| regulation of expression of symbiotic genes in rhizobium sp. ngr234. | research in the field of rhizobium-legume symbiosis faces a new challenge: integrate the wealth of information generated by genomic projects. the goal: apprehend the complexity of the molecular mechanisms involved in symbiotic associations. at the time of writing, the genomes of three micro-symbionts (bradyrhizobium japonicum, mesorhizobium loti and sinorhizobium meliloti) have been sequenced, and two more (those of rhizobium leguminosarum and rhizobium etli) will be completed in the near future ... | 2003 | 15242276 |
| a novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101. | p-nitrophenol (4-np) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. to date, several 4-np-degrading bacteria have been isolated; however, the genetic information remains very limited. in this study, a novel 4-np degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101, was identified and characterized. the deduced amino acid sequences of npcb, npca, and npcc showed identity with phenol 2-hydroxylase compon ... | 2004 | 15262926 |
| the homogentisate pathway: a central catabolic pathway involved in the degradation of l-phenylalanine, l-tyrosine, and 3-hydroxyphenylacetate in pseudomonas putida. | pseudomonas putida metabolizes phe and tyr through a peripheral pathway involving hydroxylation of phe to tyr (phhab), conversion of tyr into 4-hydroxyphenylpyruvate (tyrb), and formation of homogentisate (hpd) as the central intermediate. homogentisate is then catabolized by a central catabolic pathway that involves three enzymes, homogentisate dioxygenase (hmga), fumarylacetoacetate hydrolase (hmgb), and maleylacetoacetate isomerase (hmgc), finally yielding fumarate and acetoacetate. whereas t ... | 2004 | 15262943 |
| sequencing and analysis of the large virulence plasmid plvpk of klebsiella pneumoniae cg43. | we have determined the entire dna sequence of plvpk, which is a 219-kb virulence plasmid harbored in a bacteremic isolate of klebsiella pneumoniae. a total of 251 open reading frames (orfs) were annotated, of which 37% have homologous genes of known function, 31% match the hypothetical genes in the genbank database, and the remaining 32% are novel sequences. the obvious virulence-associated genes carried by the plasmid are the capsular polysaccharide synthesis regulator rmpa and its homolog rmpa ... | 2004 | 15276215 |
| real-time taqman pcr for quantifying oral bacteria during biofilm formation. | a taqman pcr was developed for quantifying early colonizer microorganisms in dental biofilms. to design species-specific primers and taqman probes, genomic subtractive hybridization was used. this quantitative assay in combination with subtractive hybridization may be of value in the study of microbial ecosystems consisting of related species that are involved in the formation and etiology of biofilms. | 2004 | 15297540 |
| identification and transcriptional control of caulobacter crescentus genes encoding proteins containing a cold shock domain. | the cold shock proteins are small peptides that share a conserved domain, called the cold shock domain (csd), that is important for nucleic acid binding. the caulobacter crescentus genome has four csp genes that encode proteins containing csds. three of these (cspa, cspb, and cspc) encode peptides of about 7 kda and are very similar to the cold shock proteins of other bacteria. analysis by reverse transcription-pcr of the fourth gene (cspd), which was previously annotated as encoding a 7-kda pro ... | 2004 | 15317764 |