| 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 |
| transmembrane modulator-dependent bacterial tyrosine kinase activates udp-glucose dehydrogenases. | protein-tyrosine kinases regulating bacterial exopolysaccharide synthesis autophosphorylate on tyrosines located in a conserved c-terminal region. so far no other substrates have been identified for these kinases. here we demonstrate that bacillus subtilis ywqd not only autophosphorylates at tyr-228, but that it also phosphorylates the two udp-glucose dehydrogenases (udp-glucose dhs) ywqf and tuad at a tyrosine residue. however, phosphorylation of ywqf and tuad occurs only in the presence of the ... | 2003 | 12970183 |
| specific binding of the regulatory protein expg to promoter regions of the galactoglucan biosynthesis gene cluster of sinorhizobium meliloti--a combined molecular biology and force spectroscopy investigation. | specific protein-dna interaction is fundamental for all aspects of gene transcription. we focus on a regulatory dna-binding protein in the gram-negative soil bacterium sinorhizobium meliloti 2011, which is capable of fixing molecular nitrogen in a symbiotic interaction with alfalfa plants. the expg protein plays a central role in regulation of the biosynthesis of the exopolysaccharide galactoglucan, which promotes the establishment of symbiosis. expg is a transcriptional activator of exp gene ex ... | 2003 | 12972351 |
| an improved probability mapping approach to assess genome mosaicism. | maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. however, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. here we extend the probability mapping approach by improving taxon sampling o ... | 2003 | 12974984 |
| transcriptional control of a rrna promoter of the nodulating symbiont sinorhizobium meliloti. | we constructed a stable, low-copy-number plasmid containing a fusion between a sinorhizobium meliloti rrna promoter and gfp(mut3). when transformed into s. meliloti the resulting strain, rm1021/pkw1, fluoresced in proportion to its growth rate during balanced growth. this strain also showed an unexpected behavior when grown to stationary phase in ty medium: the average cellular fluorescence increased through mid-exponential phase then decreased dramatically. the explanation for this appears to b ... | 2003 | 13129602 |
| experimental determination and system level analysis of essential genes in escherichia coli mg1655. | defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. we used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of escherichia coli in rich media. we identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. functional context analysis of these data allows individual functional assignment ... | 2003 | 13129938 |
| 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 |
| identification of three genes encoding p(ii)-like proteins in gluconacetobacter diazotrophicus: studies of their role(s) in the control of nitrogen fixation. | in our studies on the regulation of nitrogen metabolism in gluconacetobacter diazotrophicus, an endophytic diazotroph of sugarcane, three glnb-like genes were identified and their role(s) in the control of nitrogen fixation was studied. sequence analysis revealed that one p(ii) protein-encoding gene, glnb, was adjacent to a glna gene (encoding glutamine synthetase) and that two other p(ii) protein-encoding genes, identified as glnk1 and glnk2, were located upstream of amtb1 and amtb2, respective ... | 2003 | 13129958 |
| characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from burkholderia cepacia dbo1. | anthranilate (2-aminobenzoate) is an important intermediate in tryptophan metabolism. in order to investigate the degradation of tryptophan through anthranilate by burkholderia cepacia, several plasposon mutations were constructed of strain dbo1 and one mutant with the plasposon insertion in the anthranilate dioxygenase (antdo) genes was chosen for further study. the gene sequence obtained from flanking dna of the plasposon insertion site revealed unexpected information. b. cepacia dbo1 antdo (d ... | 2003 | 13129960 |
| characterization and pathogenic significance of vibrio vulnificus antigens preferentially expressed in septicemic patients. | many important virulence genes of pathogenic bacteria are preferentially expressed in vivo. we used the recently developed in vivo-induced antigen technology (iviat) to identify vibrio vulnificus genes induced in vivo. an expression library of v. vulnificus was screened by colony blot analysis by using pooled convalescent-phase serum that had been thoroughly adsorbed with in vitro-expressed v. vulnificus whole cells and lysates. twelve clones were selected, and the sequences of the insert dnas w ... | 2003 | 14500463 |
| in silico analysis of a flavohemoglobin from sinorhizobium meliloti strain 1021. | hemoglobins (hbs) have been characterized from a wide variety of eubacteria, but not from nitrogen-fixing rhizobia. our search for hb-like sequences in the sinorhizobium meliloti genome revealed that a gene coding for a flavohemoglobin (fhb) exists in s. meliloti (smfhb). computer analysis showed that smfhb and alcaligenes eutrophus fhb are highly similar and could fold into the same tertiary structure. a fnr-like box was detected upstream of the smfhb gene and mapping analysis revealed that the ... | 2003 | 14521231 |
| positive correlation between tyrosine phosphorylation of cpsd and capsular polysaccharide production in streptococcus pneumoniae. | cpsa, cpsb, cpsc, and cpsd are part of a tyrosine phosphorylation regulatory system involved in modulation of capsule synthesis in streptococcus pneumoniae and many other gram-positive and gram-negative bacteria. using an immunoblotting technique, we observed distinct laddering patterns of s. pneumoniae capsular polysaccharides of various serotypes and found that transfer of the polymer from the membrane to the cell wall was independent of size. deletion of cps2a, cps2b, cps2c, or cps2d in the s ... | 2003 | 14526017 |
| nucleotide-dependent conformational changes in the sigma54-dependent activator dctd. | activators of sigma(54)-rna polymerase holoenzyme couple atp hydrolysis to formation of an open promoter complex. dctd(delta1-142), a truncated and constitutively active form of the sigma(54)-dependent activator dctd from sinorhizobium meliloti, displayed an altered dnase i footprint at its binding site located upstream of the dcta promoter in the presence of atp. the altered footprint was not observed for a mutant protein with a substitution at or near the putative arginine finger, a conserved ... | 2003 | 14526036 |
| conditional survival as a selection strategy to identify plant-inducible genes of pseudomonas syringae. | a novel strategy termed habitat-inducible rescue of survival (hirs) was developed to identify genes of pseudomonas syringae that are induced during growth on bean leaves. this strategy is based on the complementation of metxw, two cotranscribed genes that are necessary for methionine biosynthesis and required for survival of p. syringae on bean leaves exposed to conditions of low humidity. we constructed a promoter trap vector, ptrap, containing a promoterless version of the wild-type p. syringa ... | 2003 | 14532027 |
| cloning, characterization, and functional expression of the klebsiella oxytoca xylodextrin utilization operon (xyntb) in escherichia coli. | escherichia coli is being developed as a biocatalyst for bulk chemical production from inexpensive carbohydrates derived from lignocellulose. potential substrates include the soluble xylodextrins (xyloside, xylooligosaccharide) and xylobiose that are produced by treatments designed to expose cellulose for subsequent enzymatic hydrolysis. adjacent genes encoding xylobiose uptake and hydrolysis were cloned from klebsiella oxytoca m5a1 and are functionally expressed in ethanologenic e. coli. the xy ... | 2003 | 14532050 |
| polyphasic taxonomy of symbiotic rhizobia from wild leguminous plants growing in egypt. | about 20 strains of rhizobia from wild legumes were characterized based on numerical analysis of phenotypic characteristics, nodulating ability, fatty acid methyl esters (fame) and sds-page profiles of whole cell proteins. fame analysis revealed that palmitic (16:0), stearic (18:0) and arachidonic (20:0) were detected in most of wild-legume rhizobia, the latter being uncommon in fatty acid profiles of rhizobium and sinorhizobium. numerical analysis of fame classified strains of wild-legume rhizo ... | 2003 | 14533483 |
| 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 |
| regulation of the transcriptional activator ntrc1: structural studies of the regulatory and aaa+ atpase domains. | transcription by sigma54 rna polymerase depends on activators that contain atpase domains of the aaa+ class. these activators, which are often response regulators of two-component signal transduction systems, remodel the polymerase so that it can form open complexes at promoters. here, we report the first crystal structures of the atpase domain of an activator, the ntrc1 protein from the extreme thermophile aquifex aeolicus. this domain alone, which is active, crystallized as a ring-shaped hepta ... | 2003 | 14561776 |
| bacteriophage st64b, a genetic mosaic of genes from diverse sources isolated from salmonella enterica serovar typhimurium dt 64. | the complete sequence of the double-stranded dna (dsdna) genome of the salmonella enterica serovar typhimurium st64b bacteriophage was determined. the 40,149-bp genomic sequence of st64b has an overall g+c content of 51.3% and is distinct from that of p22. the genome architecture is similar to that of the lambdoid phages, particularly that of coliphage lambda. most of the putative tail genes showed sequence similarity to tail genes of mu, a nonlambdoid phage. in addition, it is likely that these ... | 2003 | 14563886 |
| identification of a gene that affects the efficiency of host cell infection by legionella pneumophila in a temperature-dependent fashion. | the ability to infect host cells is critical for the survival and replication of intracellular pathogens in humans. we previously found that many genes involved in the ability of legionella pneumophila to infect macrophages are not expressed efficiently under standard laboratory growth conditions. we have developed an approach using expression of l. pneumophila genes from an exogenous constitutive promoter on a low-copy-number vector that allows identification of genes involved in host cell infe ... | 2003 | 14573644 |
| chemical identification of n-acyl homoserine lactone quorum-sensing signals produced by sinorhizobium meliloti strains in defined medium. | the n-acyl homoserine lactone (ahl) quorum-sensing signals produced by sinorhizobium meliloti strains ak631 and 1021 when cultured in a defined glucose-nitrate medium were identified by gas chromatography/mass spectrometry (gc/ms) and electrospray ionization tandem mass spectrometry (esi ms/ms). both strains synthesized several long-chain ahls. defined medium cultures of strain ak631 synthesized a complex mixture of ahls with short acyl side chains. strain 1021 produced no short-chain ahls when ... | 2003 | 14593447 |
| flavobacterium johnsoniae gldh is a lipoprotein that is required for gliding motility and chitin utilization. | cells of flavobacterium johnsoniae move rapidly over surfaces by gliding motility. the mechanism of this form of motility is not known. six genes (glda, gldb, gldd, gldf, gldg, and ftsx) that are required for gliding have been described. tn4351 mutagenesis was used to identify another gene, gldh, which is required for cell movement. gldh mutants formed nonspreading colonies, and individual cells lacked the cell movements and ability to propel latex spheres along their surfaces that are character ... | 2003 | 14594839 |
| the strength of translational selection for codon usage varies in the three replicons of sinorhizobium meliloti. | the genome of the nitrogen-fixing bacterium sinorhizobium meliloti is composed of three replicons of 3.65 (chromosome), 1.35 (psyma) and 1.68 mb (psymb), respectively. while the chromosome encodes for most of the housekeeping functions, the three elements may contribute to symbiosis, though psyma is absolutely necessary for nodulation and nitrogen fixation, since it harbours all the characterized nodulation and symbiotic fixation genes. on the other hand, the majority of the sequences located in ... | 2003 | 14597394 |
| 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 |
| development and application of a dapb-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium pseudomonas stutzeri a15. | pseudomonas stutzeri a15 is a nitrogen-fixing bacterium isolated from paddy rice. strain a15 is able to colonize and infect rice roots. this strain may provide rice plants with fixed nitrogen and hence promote plant growth. in this article, we describe the use of dapb-based in vivo expression technology to identify p. stutzeri a15 genes that are specifically induced during colonization and infection (cii). we focused on the identification of p. stutzeri a15 genes that are switched on during rice ... | 2003 | 14602651 |
| enzyme-specific profiles for genome annotation: priam. | the advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. here we describe priam, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the enzyme database. priam relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each enzyme entry. automatically generated logical rules define which of these profile ... | 2003 | 14602924 |
| endophytic nifh gene diversity in african sweet potato. | a cultivation-independent approach was used to identify potentially nitrogen-fixing endophytes in seven sweet potato varieties collected in uganda and kenya. nitrogenase reductase genes (nifh) were amplified by pcr, and amplicons were cloned in escherichia coli. clones were grouped by restriction fragment length polymorphism analysis, and representative nifh genes were sequenced. the resulting sequences had high homologies to nitrogenase reductases from alpha-, beta-, and gamma-proteobacteria an ... | 2003 | 14608421 |
| 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 |
| 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 |
| folm, a new chromosomally encoded dihydrofolate reductase in escherichia coli. | escherichia coli (thya deltafola) mutants are viable and can grow in minimal medium when supplemented with thymidine alone. here we present evidence from in vivo and in vitro studies that the ydgb gene determines an alternative dihydrofolate reductase that is related to the trypanosomatid pteridine reductases. we propose to rename this gene folm. | 2003 | 14617668 |
| a medicago sativa haem oxygenase gene is preferentially expressed in root nodules. | haem oxygenases (ho) are ubiquitous enzymes catalysing the oxidative degradation of haem into biliverdin, iron and carbon monoxide. whereas animal hos participate in multiple cellular functions including haemoglobin catabolism, antioxidant defence and iron homeostasis, to date, plant hos have so far only been involved in phytochrome metabolism. the expression of the ho1 gene was studied in medicago sativa, especially during the interaction with its symbiotic partner, sinorhizobium meliloti. tran ... | 2004 | 14623903 |
| characterization of four lectin-like receptor kinases expressed in roots of medicago truncatula. structure, location, regulation of expression, and potential role in the symbiosis with sinorhizobium meliloti. | to study the role of lecrk (lectin-like receptor kinase) genes in the legumerhizobia symbiosis, we have characterized the four medicago truncatula gaernt. lecrk genes that are most highly expressed in roots. three of these genes, mtlecrk7;1, mtlecrk7;2, and mtlecrk7;3, encode proteins most closely related to the class a lecrks of arabidopsis, whereas the protein encoded by the fourth gene, mtlecrk1;1, is most similar to a class b arabidopsis lecrk. all four genes show a strongly enhanced root ex ... | 2003 | 14630957 |
| the mycobacterium tuberculosis complex-restricted gene cfp32 encodes an expressed protein that is detectable in tuberculosis patients and is positively correlated with pulmonary interleukin-10. | human tuberculosis (tb) is caused by the bacillus mycobacterium tuberculosis, a subspecies of the m. tuberculosis complex (mtc) of mycobacteria. postgenomic dissection of the m. tuberculosis proteome is ongoing and critical to furthering our understanding of factors mediating m. tuberculosis pathobiology. towards this end, a 32-kda putative glyoxalase in the culture filtrate (cf) of growing m. tuberculosis (originally annotated as rv0577 and hereafter designated cfp32) was identified, cloned, an ... | 2003 | 14638775 |
| identification and characterization of ppta: a gene involved in the phase-variable expression of phosphorylcholine on pili of neisseria meningitidis. | pili of pathogenic neisseria are major virulence factors associated with adhesion, cytotoxicity, twitching motility, autoaggregation, and dna transformation. pili are modified posttranslationally by the addition of phosphorylcholine. however, no genes involved in either the biosynthesis or the transfer of phosphorylcholine in neisseria meningitidis have been identified. in this study, we identified five candidate open reading frames (orfs) potentially involved in the biosynthesis or transfer of ... | 2003 | 14638777 |
| functional analysis of the mycobacterium tuberculosis mprab two-component signal transduction system. | the mechanisms utilized by mycobacterium tuberculosis to establish, maintain, or reactivate from latent infection in the host are largely unknown but likely include genes that mediate adaptation to conditions encountered during persistence. previously, a two-component signal transduction system, mprab, was found to be required in m. tuberculosis for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. to begin to characterize the role of this system in m ... | 2003 | 14638785 |
| 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 |
| legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature. | following the initial discovery of two legume-nodulating burkholderia strains (l. moulin, a. munive, b. dreyfus, and c. boivin-masson, nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of burkholderia caribensis and ralstonia taiwanensis, all belonging to the beta-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. r. taiwanensis was found to represent 93% of the mimosa isolates in taiwan, indicating that ... | 2003 | 14645288 |
| construction and validation of a sinorhizobium meliloti whole genome dna microarray: genome-wide profiling of osmoadaptive gene expression. | based on the complete sinorhizobium meliloti genome sequence we established dna microarrays as a comprehensive tool for systematic genome-wide gene expression analysis in s. meliloti 1021. for these pcr fragment-based microarrays, called sm6kpcr, a collection of probes for the 6207 predicted protein-coding genes consisting of 6046 gene-specific pcr fragments and 161 70 mer oligonucleotides was arrayed in high density on glass slides. to obtain these pcr fragments primer pairs were designed to am ... | 2003 | 14651866 |
| the genus name ensifer casida 1982 takes priority over sinorhizobium chen et al. 1988, and sinorhizobium morelense wang et al. 2002 is a later synonym of ensifer adhaerens casida 1982. is the combination "sinorhizobium adhaerens" (casida 1982) willems et al. 2003 legitimate? request for an opinion. | the synonymy of the genera ensifer and sinorhizobium was recently reported, but it was proposed that the later-named genus, sinorhizobium, take priority in nomenclature. there is no justification in the international code of nomenclature of bacteria (prokaryotes) for this step; ensifer is the correct name of the genus, with ensifer adhaerens as the type species. species previously allocated to sinorhizobium are here proposed as the new combinations ensifer arboris, ensifer fredii, ensifer kostie ... | 2003 | 14657154 |
| 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 |
| molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. | isolates belonging to six genera not previously known to oxidize co were obtained from enrichments with aquatic and terrestrial plants. dna from these and other isolates was used in pcr assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxl). coxl and putative coxl fragments were amplified from known co oxidizers (e.g., oligotropha carboxidovorans and bradyrhizobium japonicum), from novel co-oxidizing isolates (e.g., aminobacter sp. strain cox, burkholderia sp. strain lu ... | 2003 | 14660374 |
| 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 |
| pathways for phosphatidylcholine biosynthesis in bacteria. | phosphatidylcholine (pc) is the major membrane-forming phospholipid in eukaryotes with important structural and signalling functions. although many prokaryotes lack pc, it can be found in significant amounts in membranes of rather diverse bacteria. two pathways for pc biosynthesis are known in bacteria, the methylation pathway and the phosphatidylcholine synthase (pcs) pathway. in the methylation pathway, phosphatidylethanolamine is methylated three times to yield pc, in reactions catalysed by o ... | 2003 | 14663079 |
| two dictyostelium orthologs of the prokaryotic cell division protein ftsz localize to mitochondria and are required for the maintenance of normal mitochondrial morphology. | in bacteria, the protein ftsz is the principal component of a ring that constricts the cell at division. though all mitochondria probably arose through a single, ancient bacterial endosymbiosis, the mitochondria of only certain protists appear to have retained ftsz, and the protein is absent from the mitochondria of fungi, animals, and higher plants. we have investigated the role that ftsz plays in mitochondrial division in the genetically tractable protist dictyostelium discoideum, which has tw ... | 2003 | 14665465 |
| 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 |
| chlamydomonas reinhardtii secretes compounds that mimic bacterial signals and interfere with quorum sensing regulation in bacteria. | the unicellular soil-freshwater alga chlamydomonas reinhardtii was found to secrete substances that mimic the activity of the n-acyl-l-homoserine lactone (ahl) signal molecules used by many bacteria for quorum sensing regulation of gene expression. more than a dozen chemically separable but unidentified substances capable of specifically stimulating the lasr or cepr but not the luxr, ahyr, or cvir ahl bacterial quorum sensing reporter strains were detected in ethyl acetate extracts of c. reinhar ... | 2004 | 14671013 |
| mosa, a protein implicated in rhizopine biosynthesis in sinorhizobium meliloti l5-30, is a dihydrodipicolinate synthase. | mosa is a gene product encoded on a psym megaplasmid of sinorhizobium meliloti l5-30. the gene is part of an operon reported to be essential for the synthesis of the rhizopine 3-o-methyl-scyllo-inosamine. mosa has been assigned the function of an o-methyltransferase. however, the reported sequence of this protein is very much like that of dihydrodipicolinate synthase (dhdps), except for a 40 amino acid residue c-terminal domain. this similarity contradicts accepted ideas regarding structure-func ... | 2004 | 14672649 |
| metabolic reconstruction of sulfur assimilation in the extremophile acidithiobacillus ferrooxidans based on genome analysis. | acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at ph2 and obtains energy by the oxidation of sulfur and iron. it is used in the biomining industry for the recovery of metals and is one of the causative agents of acid mine drainage. effective tools for the study of its genetics and physiology are not in widespread use and, despite considerable effort, an understanding of its unusual physiology remains at a rudimentary level. nearly complete genome sequences of a. ferrooxidan ... | 2003 | 14675496 |
| 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 |
| [the biological activity of the sinorhizobium meliloti glucan]. | the study of the effect of the periplasmic glucan isolated from the root-nodule bacterium s. meliloti cxm1-188 on the symbiosis of another strain (441) of the same root-nodule bacterium with alfalfa plants showed that this effect depends on the treatment procedure. the pretreatment of alfalfa seedlings with the glucan followed by their bacterization with s. meliloti 441 insignificantly influenced the nodulation parameters of symbiosis (the number of root nodules and their nitrogen-fixing activit ... | 2003 | 14679901 |
| glucose 6-phosphate dehydrogenase is required for sucrose and trehalose to be efficient osmoprotectants in sinorhizobium meliloti. | inactivation of the zwf gene in sinorhizobium meliloti induces an osmosensitive phenotype and the loss of osmoprotection by trehalose and sucrose, but not by ectoine and glycine betaine. this phenotype is not linked to a defect in the biosynthesis of endogenous solutes. zwf expression is induced by high osmolarity, sucrose and trehalose, but is repressed by betaine. a zwf mutant is more sensitive than its parental strain to superoxide ions, suggesting that glucose 6-phosphate dehydrogenase invol ... | 2003 | 14680697 |
| role of siderophore biosynthesis in virulence of staphylococcus aureus: identification and characterization of genes involved in production of a siderophore. | molecular determinants underlying the production of siderophores in the human and animal pathogen staphylococcus aureus and the contribution of siderophore production to the virulence of this bacterium have, until now, remained undefined. here, we show that s. aureus strains rn6390 and newman produce siderophore when the cells are starved for iron. we further identified and characterized a nine-gene, iron-regulated operon, designated sbn and situated between sirabc and gale on the s. aureus chro ... | 2004 | 14688077 |
| osmoregulatory systems of escherichia coli: identification of betaine-carnitine-choline transporter family member betu and distributions of betu and trkg among pathogenic and nonpathogenic isolates. | multiple transporters mediate osmoregulatory solute accumulation in escherichia coli k-12. the larger genomes of naturally occurring strains such as pyelonephritis isolates cft073 and hu734 may encode additional osmoregulatory systems. cft073 is more osmotolerant than hu734 in the absence of organic osmoprotectants, yet both strains grew in high osmolality medium at low k(+) (micromolar concentrations) and retained locus trkh, which encodes an osmoregulatory k(+) transporter. both lacked the trk ... | 2004 | 14702297 |
| complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage d3112. | bacteriophage d3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen pseudomonas aeruginosa. to further our understanding of transposable phage in p. aeruginosa, we have sequenced the complete genome of d3112. the genome is 37,611 bp, with an overall g+c content of 65%. we have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes a and b) that have been previously characterized ... | 2004 | 14702309 |
| 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 |
| variable bacteriocin production in the commercial starter lactococcus lactis dpc4275 is linked to the formation of the cointegrate plasmid pmrc02. | lactococcus lactis dpc4275 is a bacteriocin-producing transconjugant of the industrial starter strain dpc4268. strain dpc4275 was generated through conjugal transfer by mating dpc4268 with l. lactis mg1363 containing the 60-kb plasmid pmrc01, which encodes the genetic determinants for the lantibiotic lacticin 3147 and for a phage resistance mechanism of the abortive infection type. the many significant applications of this strain prompted a genetic analysis of its apparently unstable bacteriocin ... | 2004 | 14711623 |
| molecular cloning, purification, and biochemical characterization of hydantoin racemase from the legume symbiont sinorhizobium meliloti cect 4114. | hydantoin racemase from sinorhizobium meliloti was functionally expressed in escherichia coli. the native form of the enzyme was a homotetramer with a molecular mass of 100 kda. the optimum temperature and ph for the enzyme were 40 degrees c and 8.5, respectively. the enzyme showed a slight preference for hydantoins with short rather than long aliphatic side chains or those with aromatic rings. substrates, which showed no detectable activity toward the enzyme, were found to exhibit competitive i ... | 2004 | 14711700 |
| expression of mslec1 transgenes in alfalfa plants causes symbiotic abnormalities. | legume lectins have been proposed to have important symbiotic roles during rhizobium-legume symbioses. to test this hypothesis, the symbiotic responses of transgenic alfalfa plants that express a portion of the putative alfalfa lectin gene mslec1 or mslec2 in either the antisense or sense orientation were analyzed following inoculation with wild-type sinorhizobium meliloti 1021. mslec1-antisense (lec1as) plants were stunted, exhibited hypernodulation, and developed not only abnormally large nodu ... | 2004 | 14714864 |
| a two-component signal transduction system with a pas domain-containing sensor is required for virulence of mycobacterium tuberculosis in mice. | mycobacterium tuberculosis, the causative organism of tuberculosis, encounters oxidative stress during phagocytosis by the macrophage and following macrophage activation during an acquired immune response, and also from internally generated sources of radical oxygen intermediates through intermediary metabolism. we have identified the senx3 protein, a sensor in 1 of the 11 complete pairs of two-component signal transduction systems in m. tuberculosis, as a possible orthologue of the mak2p protei ... | 2004 | 14715274 |
| a functional cellulose synthase from ascidian epidermis. | among animals, urochordates (e.g., ascidians) are unique in their ability to biosynthesize cellulose. in ascidians cellulose is synthesized in the epidermis and incorporated into a protective coat know as the tunic. a putative cellulose synthase-like gene was first identified in the genome sequences of the ascidian ciona intestinalis. we describe here a cellulose synthase gene from the ascidian ciona savignyi that is expressed in the epidermis. the predicted c. savignyi cellulose synthase amino ... | 2004 | 14722352 |
| rhodobacter capsulatus nifa1 promoter: high-gc -10 regions in high-gc bacteria and the basis for their transcription. | it was previously shown that the rhodobacter capsulatus ntrc enhancer-binding protein activates the r. capsulatus housekeeping rna polymerase but not the escherichia coli rna polymerase at the nifa1 promoter. we have tested the hypothesis that this activity is due to the high g+c content of the -10 sequence. a comparative analysis of r. capsulatus and other alpha-proteobacterial promoters with known transcription start sites suggests that the g+c content of the -10 region is higher than that for ... | 2004 | 14729700 |
| 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 |
| plant and bacterial symbiotic mutants define three transcriptionally distinct stages in the development of the medicago truncatula/sinorhizobium meliloti symbiosis. | in the medicago truncatula/sinorhizobium meliloti symbiosis, the plant undergoes a series of developmental changes simultaneously, creating a root nodule and allowing bacterial entry and differentiation. our studies of plant genes reveal novel transcriptional regulation during the establishment of the symbiosis and identify molecular markers that distinguish classes of plant and bacterial symbiotic mutants. we have identified three symbiotically regulated plant genes encoding a beta,1-3 endogluc ... | 2004 | 14739349 |
| bacillus subtilis chec and fliy are members of a novel class of chey-p-hydrolyzing proteins in the chemotactic signal transduction cascade. | rapid restoration of prestimulus levels of the chemotactic response regulator, chey-p, is important for preparing bacteria and archaea to respond sensitively to new stimuli. in an extension of previous work (szurmant, h., bunn, m. w., cannistraro, v. j., and ordal, g. w. (2003) j. biol. chem. 278, 48611-48616), we describe a new family of chey-p phosphatases, the cyx family, that is widespread among the bacteria and archaea. these proteins provide another pathway, in addition to the ones involvi ... | 2004 | 14749334 |
| the roles of different regions of the cych protein in c-type cytochrome biogenesis in sinorhizobium meliloti. | cytochrome c heme lyases encoded by the sinorhizobium meliloti cychjkl operon are responsible for generating the covalent bond between the heme prosthetic group and apocytochromes c. the cych protein with its presumably membrane-associated n-terminal and periplasmic c-terminal parts is thought to be responsible for binding apocytochrome and presenting it to the heme ligation machinery. we propose that these two modules of cych play roles in different functions of the protein. the n-terminal 96 a ... | 2004 | 14758542 |
| mutational analysis of gsti protein, a glutamine synthetase translational inhibitor of rhizobium leguminosarum. | the small gsti protein (63 amino acids) of rhizobium leguminosarum inhibits the expression of the glnii (glutamine synthetase ii) gene, thus reducing the bacterial ability to assimilate ammonium. in order to identify the residues essential for its inhibitory activity, all the 53 non-alanine amino acid residues of gsti were individually mutated into alanine. based on their capacity to inhibit glnii expression (in two genetic backgrounds) three groups of mutants were identified. the first group di ... | 2004 | 14759514 |
| biochemical characterization of symbiosome membrane proteins from medicago truncatula root nodules. | the symbiosome membrane represents a specialized plant membrane that forms both a structural and a functional interface between the legume plant and its bacterial counterpart. in this study, the symbiosome membrane protein profile from the model system medicago truncatula and the corresponding bacterium sinorhizobium meliloti was examined using two-dimensional electrophoresis and microcapillary high-performance liquid chromatography (hplc) tandem mass spectrometry. the identities of 51 proteins ... | 2004 | 14760646 |
| myxococcus xanthus chemotaxis homologs difd and difg negatively regulate fibril polysaccharide production. | the extracellular matrix fibrils of myxococcus xanthus are essential for the social lifestyle of this unusual bacterium. these fibrils form networks linking or encasing cells and are tightly correlated with cellular cohesion, development, and social (s) gliding motility. previous studies identified a set of bacterial chemotaxis homologs encoded by the dif locus. it was determined that difa, difc, and dife, encoding respective homologs of a methyl-accepting chemotaxis protein, chew, and chea, are ... | 2004 | 14761994 |
| differential expression of two paralogous genes of bacillus subtilis encoding single-stranded dna binding protein. | the bacillus subtilis genome comprises two paralogous single-stranded dna binding protein (ssb) genes, ssb and ywph, which show distinct expression patterns. the main ssb gene is strongly expressed during exponential growth and is coregulated with genes encoding the ribosomal proteins s6 and s18. the gene organization rpsf-ssb-rpsr as observed in b. subtilis is found in many gram-positive as well as some gram-negative bacteria, but not in escherichia coli. the ssb gene is essential for cell viab ... | 2004 | 14762004 |
| 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 |
| distribution and phylogenetic analysis of family 19 chitinases in actinobacteria. | in organisms other than higher plants, family 19 chitinase was first discovered in streptomyces griseus hut6037, and later, the general occurrence of this enzyme in streptomyces species was demonstrated. in the present study, the distribution of family 19 chitinases in the class actinobacteria and the phylogenetic relationship of actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. forty-nine strains were chosen to cover almost all the suborders of ... | 2004 | 14766598 |
| phospholipid synthesis in borrelia burgdorferi: bb0249 and bb0721 encode functional phosphatidylcholine synthase and phosphatidylglycerolphosphate synthase proteins. | phospholipids are an important component of bacterial membranes. borrelia burgdorferi differs from many other bacteria in that it contains only two major membrane phospholipids: phosphatidylglycerol (pg) and phosphatidylcholine (pc). b. burgdorferi appears to lack enzymes required for synthesis of pc through the well-described methylation pathway. however, b. burgdorferi does contain a gene (bb0249) with significant identity to a recently described phosphatidylcholine synthase gene (pcs) of sino ... | 2004 | 14766917 |
| the key sinorhizobium meliloti succinoglycan biosynthesis gene exoy is expressed from two promoters. | bacterial exopolysaccharide, succinoglycan, plays an important role in eliciting infection thread formation, which is a key step in the establishment of sinorhizobium meliloti-alfalfa (medicago sativa) nitrogen fixing symbiosis. to understand the regulatory mechanisms that control production of succinoglycan, the expression of the key succinoglycan biosynthesis gene, exoy, was analyzed by constructing a set of nested deletions of the exoy promoter region. two exoy promoters were identified based ... | 2004 | 14769477 |
| design and diversity in bacterial chemotaxis: a comparative study in escherichia coli and bacillus subtilis. | comparable processes in different species often involve homologous genes. one question is whether the network structure, in particular the feedback control structure, is also conserved. the bacterial chemotaxis pathways in e. coli and b. subtilis both regulate the same task, namely, excitation and adaptation to environmental signals. both pathways employ many orthologous genes. yet how these orthologs contribute to network function in each organism is different. to investigate this problem, we p ... | 2004 | 14966542 |
| adp reduces the oxygen-binding affinity of a sensory histidine kinase, fixl: the possibility of an enhanced reciprocating kinase reaction. | the rhizobial fixl/fixj system, a paradigm of heme-based oxygen sensors, belongs to the ubiquitous two-component signal transduction system. oxygen-free (deoxy) fixl is autophosphorylated at an invariant histidine residue by using atp and catalyzes the concomitant phosphoryl transfer to fixj, but oxygen binding to the fixl heme moiety inactivates the kinase activity. here we demonstrate that adp acts as an allosteric effector, reducing the oxygen-binding affinity of the sensor domain in fixl whe ... | 2004 | 14970341 |
| 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 |
| 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 |
| in silico and transcriptional analysis of carbohydrate uptake systems of streptomyces coelicolor a3(2). | streptomyces coelicolor is the prototype for the investigation of antibiotic-producing and differentiating actinomycetes. as soil bacteria, streptomycetes can metabolize a wide variety of carbon sources and are hence vested with various specific permeases. their activity and regulation substantially determine the nutritional state of the cell and, therefore, influence morphogenesis and antibiotic production. we have surveyed the genome of s. coelicolor a3(2) to provide a thorough description of ... | 2004 | 14973030 |
| molecular and biochemical analysis of two cdna clones encoding dihydroflavonol-4-reductase from medicago truncatula. | dihydroflavonol-4-reductase (dfr; ec1.1.1.219) catalyzes a key step late in the biosynthesis of anthocyanins, condensed tannins (proanthocyanidins), and other flavonoids important to plant survival and human nutrition. two dfr cdna clones (mtdfr1 and mtdfr2) were isolated from the model legume medicago truncatula cv jemalong. both clones were functionally expressed in escherichia coli, confirming that both encode active dfr proteins that readily reduce taxifolin (dihydroquercetin) to leucocyanid ... | 2004 | 14976232 |
| a second tylosin resistance determinant, erm b, in arcanobacterium pyogenes. | arcanobacterium pyogenes, a common inhabitant of the mucosal surfaces of livestock, is also a pathogen associated with a variety of infections. in livestock, a. pyogenes is exposed to antimicrobial agents used for prophylaxis and therapy, notably tylosin, a macrolide used extensively for the prevention of liver abscessation in feedlot cattle in the united states. many, but not all, tylosin-resistant a. pyogenes isolates carry erm(x), suggesting the presence of other determinants of tylosin resis ... | 2004 | 14982756 |
| a bipolar dna helicase gene, hera, clusters with rad50, mre11 and nura genes in thermophilic archaea. | we showed previously that rad50 and mre11 genes of thermophilic archaea are organized in an operon-like structure with a third gene (nura) encoding a 5' to 3' exonuclease. here, we show that the rad50, mre11 and nura genes from the hyperthermophilic archaeon sulfolobus acidocaldarius are co-transcribed with a fourth gene encoding a dna helicase. this enzyme (hera) is the prototype of a new class of dna helicases able to utilize either 3' or 5' single-stranded dna extensions for loading and subse ... | 2004 | 14990749 |
| smc01944, a secreted peroxidase induced by oxidative stresses in sinorhizobium meliloti 1021. | sequencing of the sinorhizobium meliloti strain 1021 genome led to the detection of 6204 open reading frames, 41 % of which have no hypothetical function. to help annotate this genome, a transcriptome analysis was carried out with a dedicated microarray consisting of 146 genes belonging to three different classes: (i) no hypothetical function; (ii) potentially involved in oxidative stress responses; (iii) known to participate in oxidative stress responses (e.g. catalase and superoxide dismutase ... | 2004 | 14993315 |
| 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 |
| phosphatidylethanolamine is not essential for growth of sinorhizobium meliloti on complex culture media. | in addition to phosphatidylglycerol (pg), cardiolipin (cl), and phosphatidylethanolamine (pe), sinorhizobium meliloti also possesses phosphatidylcholine (pc) as a major membrane lipid. the biosynthesis of pc in s. meliloti can occur via two different routes, either via the phospholipid n-methylation pathway, in which pe is methylated three times in order to obtain pc, or via the phosphatidylcholine synthase (pcs) pathway, in which choline is condensed with cdp-diacylglycerol to obtain pc directl ... | 2004 | 14996797 |
| the typa gene is required for stress adaptation as well as for symbiosis of sinorhizobium meliloti 1021 with certain medicago truncatula lines. | in this article, we describe the typa gene of sinorhizobium meliloti, the orthologue of typa/bipa genes found in a wide range of bacteria. we found that typa was required for survival of s. meliloti under certain stress conditions, such as growth at low temperature or low ph and in the presence of sodium dodecyl sulfate (sds). the cold-sensitive phenotype of both escherichia coli bipa and s. meliloti typa mutants were cross-complemented, indicating that the two genes are functionally equivalent. ... | 2004 | 15000390 |
| global changes in gene expression in sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. | sinorhizobium meliloti is an alpha-proteobacterium that alternates between a free-living phase in bulk soil or in the rhizosphere of plants and a symbiotic phase within the host plant cells, where the bacteria ultimately differentiate into nitrogen-fixing organelle-like cells, called bacteroids. as a step toward understanding the physiology of s. meliloti in its free-living and symbiotic forms and the transition between the two, gene expression profiles were determined under two sets of biologic ... | 2004 | 15000396 |
| visualization of the phylogenetic content of five genomes using dekapentagonal maps. | the methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. if the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. analyses of genomes representing five photosynthetic ... | 2004 | 15003123 |
| 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 |
| 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 |
| sinorhizobium meliloti rpoh1 is required for effective nitrogen-fixing symbiosis with alfalfa. | sinorhizobium meliloti is a root-nodulating, nitrogen-fixing bacterium. an s. meliloti strain that is mutant for the rpoh(1) gene, which encodes a sigma(32)-like protein, elicits the formation of ineffective nodules on the host plant alfalfa. we characterized the rpoh(1) mutant for phenotypes related to symbiosis. alfalfa nodules formed by the rpoh(1) mutant exhibited greatly reduced levels of acetylene reduction activity compared to the wild-type nodules. whereas intracellular colonization by r ... | 2004 | 15007732 |
| a bifunctional 3,5-epimerase/4-keto reductase for nucleotide-rhamnose synthesis in arabidopsis. | l-rhamnose is a component of plant cell wall pectic polysaccharides, diverse secondary metabolites, and some glycoproteins. the biosynthesis of the activated nucleotide-sugar form(s) of rhamnose utilized by the various rhamnosyltransferases is still elusive, and no plant enzymes involved in their synthesis have been purified. in contrast, two genes (rmlc and rmld) have been identified in bacteria and shown to encode a 3,5-epimerase and a 4-keto reductase that together convert dtdp-4-keto-6-deoxy ... | 2004 | 15020741 |
| 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 |
| dna sequence duplication in rhodobacter sphaeroides 2.4.1: evidence of an ancient partnership between chromosomes i and ii. | the complex genome of rhodobacter sphaeroides 2.4.1, composed of chromosomes i (ci) and ii (cii), has been sequenced and assembled. we present data demonstrating that the r. sphaeroides genome possesses an extensive amount of exact dna sequence duplication, 111 kb or approximately 2.7% of the total chromosomal dna. the chromosomal dna sequence duplications were aligned to each other by using mummer. frequency and size distribution analyses of the exact dna duplications revealed that the interchr ... | 2004 | 15028685 |
| the fixabcx genes in rhodospirillum rubrum encode a putative membrane complex participating in electron transfer to nitrogenase. | in our efforts to identify the components participating in electron transport to nitrogenase in rhodospirillum rubrum, we used mini-tn5 mutagenesis followed by metronidazole selection. one of the mutants isolated, snt-1, exhibited a decreased growth rate and about 25% of the in vivo nitrogenase activity compared to the wild-type values. the in vitro nitrogenase activity was essentially wild type, indicating that the mutation affects electron transport to nitrogenase. sequencing showed that the t ... | 2004 | 15028689 |
| a dna adenine methyltransferase of escherichia coli that is cell cycle regulated and essential for viability. | dna sequence analysis revealed that the putative yhdj dna methyltransferase gene of escherichia coli is 55% identical to the nostoc sp. strain pcc7120 gene encoding dna methyltransferase avaiii, which methylates adenine in the recognition sequence, atgcat. the yhdj gene was cloned, and the enzyme was overexpressed and purified. methylation and restriction analysis showed that the dna methyltransferase methylates the first adenine in the sequence atgcat. this dna methylation was found to be regul ... | 2004 | 15028690 |
| a nonsymbiotic root hair tip growth phenotype in nork-mutated legumes: implications for nodulation factor-induced signaling and formation of a multifaceted root hair pocket for bacteria. | the medicago truncatula does not make infections (dmi2) mutant is mutated in the nodulation receptor-like kinase, nork. here, we report that nork-mutated legumes of three species show an enhanced touch response to experimental handling, which results in a nonsymbiotic root hair phenotype. when care is taken not to induce this response, dmi2 root hairs respond morphologically like the wild type to nodulation factor (nf). global nf application results in root hair deformation, and nf spot applicat ... | 2004 | 15031407 |
| 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 |