Publications

weeds, worms, and more. papain's long-lost cousin, phytochelatin synthase.		2004	15375203
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
bacteroid proline catabolism affects n(2) fixation rate of drought-stressed soybeans.	in prior work, we observed that soybean (glycine max l. cv merr.) seeds inoculated with a mutant bradyrhizobium japonicum strain unable to catabolize pro (pro dehydrogenase(-) [prodh(-)]) resulted in plants that, when forced to depend on n(2) fixation as the sole source of nitrogen and subjected to mild drought stress, suffered twice as large a loss in seed yield as did plants inoculated with the parental strain. here, we used a continuous gas flow system to measure h(2) evolution as a function ...	2004	15448193
[effect of aboriginal populations of soy nodule bacteria on symbiotic activity of introduced strain bradyrhizobium japonicum 634b].	the method of limit dilutions was used to determine the number of soy nodule bacteria in soils of different regions of ukraine. symbiotic properties of aboriginal populations of soy rhizobia have been studied under the conditions of vegetation researches, their effect on activity of the introduced strain b. japonicum 634b has been shown. numerous aboriginal populations of soy nodule bacteria (200-3500 units per 1 g of soil) have been found in soils of fields where soy was sown during a long peri ...	2004	15456214
is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways.	quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. recently, it has been proposed that autoinducer-2 (ai-2), a furanosyl borate diester derived from the recycling of s-adenosyl-homocysteine (sah) to homocysteine, serves as a universal signal for interspecies communication.	2004	15456522
effect of soil bradyrhizobia on the success of soybean inoculant strain cb 1809.	four decades of soybean [glycine max (l.) merr.] cultivation in south africa has resulted in the establishment of populations of bradyrhizobia against which the recently introduced inoculant strain cb 1809 must compete. serological and dna fingerprinting methods were used to study the diversity of nodule isolates from soils at bergville, koedoeskop and morgenzon. dominant serogroups included bradyrhizobium elkanii serotype 76 at bergville (67%), bradyrhizobium japonicum serotype 123 at morgenzon ...	2004	15462522
replicon-specific regulation of small heat shock genes in agrobacterium tumefaciens.	four genes coding for small heat shock proteins (shsps) were identified in the genome sequence of agrobacterium tumefaciens, one on the circular chromosome (hspc), one on the linear chromosome (hspl), and two on the pat plasmid (hspat1 and hspat2). induction of shsps at elevated temperatures was revealed by immunoblot analyses. primer extension experiments and translational lacz fusions demonstrated that expression of the pat-derived genes and hspl is controlled by temperature in a regulon-speci ...	2004	15466035
thermophilic, reversible gamma-resorcylate decarboxylase from rhizobium sp. strain mtp-10005: purification, molecular characterization, and expression.	we found the occurrence of thermophilic reversible gamma-resorcylate decarboxylase (gamma-rdc) in the cell extract of a bacterium isolated from natural water, rhizobium sp. strain mtp-10005, and purified the enzyme to homogeneity. the molecular mass of the enzyme was determined to be about 151 kda by gel filtration, and that of the subunit was 37.5 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; in other words, the enzyme was a homotetramer. the enzyme was induced specifically ...	2004	15466039
functional expression of sinorhizobium meliloti bets, a high-affinity betaine transporter, in bradyrhizobium japonicum usda110.	among the rhizobiaceae, bradyrhizobium japonicum strain usda110 appears to be extremely salt sensitive, and the presence of glycine betaine cannot restore its growth in medium with an increased osmolarity (e. boncompagni, m. osteras, m. c. poggi, and d. le rudulier, appl. environ. microbiol. 65:2072-2077, 1999). in order to improve the salt tolerance of b. japonicum, cells were transformed with the bets gene of sinorhizobium meliloti. this gene encodes a major glycine betaine/proline betaine tra ...	2004	15466533
unexpectedly diverse mesorhizobium strains and rhizobium leguminosarum nodulate native legume genera of new zealand, while introduced legume weeds are nodulated by bradyrhizobium species.	the new zealand native legume flora are represented by four genera, sophora, carmichaelia, clianthus, and montigena. the adventive flora of new zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in new zealand. the success of the introduced species may be due, at least in part, to the nature of their rhizobial sym ...	2004	15466541
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
the complete genomic sequence of nocardia farcinica ifm 10152.	we determined the genomic sequence of nocardia farcinica ifm 10152, a clinical isolate, and revealed the molecular basis of its versatility. the genome consists of a single circular chromosome of 6,021,225 bp with an average g+c content of 70.8% and two plasmids of 184,027 (pnf1) and 87,093 (pnf2) bp with average g+c contents of 67.2% and 68.4%, respectively. the chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as w ...	2004	15466710
heterologous complementation of the exopolysaccharide synthesis and carbon utilization phenotypes of sinorhizobium meliloti rm1021 polyhydroxyalkanoate synthesis mutants.	a reduced exopolysaccharide phenotype is associated with inability to synthesize polyhydroxyalkanaote (pha) stores in sinorhizobium meliloti strain rm1021. loss of function mutations in phbb and phbc result in non-mucoid colony morphology on yeast mannitol agar, compared to the mucoid phenotype exhibited by the parental strain. this phenotype is attributed to reduction in succinoglycan synthesis. we have used complementation of this phenotype and the previously described d-3-hydroxybutyrate/acet ...	2004	15476977
codon usage bias from trna's point of view: redundancy, specialization, and efficient decoding for translation optimization.	the selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and trna content in the framework of translation optimization. because most studies have focused only on codon usage, we analyzed the trna gene pool of 102 bacterial species. we show that as minimal generation times get shorter, the genomes contain more trna genes, but fewer anticodon species. surprisingly, despite the wide g+c variation of ...	2004	15479947
the completely sequenced plasmid pest4011 contains a novel incp1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation.	the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading bacterium achromobacter xylosoxidans subsp. denitrificans strain est4002 contains plasmid pest4011. this plasmid ensures its host a stable 2,4-d(+) phenotype. we determined the complete 76,958-bp nucleotide sequence of pest4011. this plasmid is a deletion and duplication derivative of pd2m4, the 95-kb highly unstable laboratory ancestor of pest4011, and was self-generated during different laboratory manipulations performed to increas ...	2004	15489427
maturation of the unusual single-cysteine (xxxch) mitochondrial c-type cytochromes found in trypanosomatids must occur through a novel biogenesis pathway.	the c-type cytochromes are characterized by the covalent attachment of haem to the polypeptide via thioether bonds formed from haem vinyl groups and, normally, the thiols of two cysteines in a cxxch motif. intriguingly, the mitochondrial cytochromes c and c1 from two euglenids and the trypanosomatidae contain only a single cysteine within the haem-binding motif (xxxch). there are three known distinct pathways by which c-type cytochromes are matured post-translationally in different organisms. th ...	2004	15500440
characterization of phylogenetically distant members of the adenylate cyclase family from mycobacteria: rv1647 from mycobacterium tuberculosis and its orthologue ml1399 from m. leprae.	analysis of the genome sequence of mycobacterium tuberculosis h37rv has identified 16 genes that are similar to the mammalian adenylate and guanylate cyclases. rv1647 was predicted to be an active adenylate cyclase but its position in a phylogenetically distant branch from the other enzymes characterized so far from m. tuberculosis makes it an interestingly divergent nucleotide cyclase to study. in agreement with its divergence at the sequence level from other nucleotide cyclases, the cloning, e ...	2005	15500449
a novel genetic locus outside the symbiotic island is required for effective symbiosis of bradyrhizobium japonicum with soybean glycine max.	in order to investigate the symbiotic interaction between soybean and bradyrhizobium japonicum, tnphoa mutagenesis of the microsymbiont was performed. mutant strain 2-10 was found to induce a strongly reduced number of ineffective nodules. ultrastructural analysis of the soybean nodule central tissue revealed the presence of numerous starch granules and vacuoles in the infected cells. in addition, the number of symbiosomes was extremely low, indicating an impaired interaction between the plant a ...	2004	15501655
oxa-60, a chromosomal, inducible, and imipenem-hydrolyzing class d beta-lactamase from ralstonia pickettii.	a chromosomally encoded oxacillinase, oxa-22, had been characterized from ralstonia pickettii pic-1 that did not explain by itself the resistance profile of this strain to beta-lactams. thus, further analysis of the genetic background of this species led to the identification of another oxacillinase, oxa-60, that was expressed only after beta-lactam induction. this chromosomally encoded oxacillinase shared 19% amino acid identity with oxa-22. it has a narrow-spectrum hydrolysis profile that incl ...	2004	15504844
functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading rhodococcus sp. strain rha1.	rhodococcus sp. strain rha1, a potent polychlorinated-biphenyl (pcb)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. as part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the rha1 plasmids, prhl3. the plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (orf) that is simi ...	2004	15516593
inactivation of an abc transporter gene, mcyh, results in loss of microcystin production in the cyanobacterium microcystis aeruginosa pcc 7806.	the cyanobacterium microcystis aeruginosa is widely known for its production of the potent hepatotoxin microcystin. microcystin is synthesized nonribosomally by the thiotemplate function of a large, modular enzyme complex encoded within the 55-kb microcystin synthetase (mcy) gene cluster. also encoded within the mcy gene cluster is a putative atp binding cassette (abc) transporter, mcyh. this study details the bioinformatic and mutational analyses of mcyh and offers functional predictions for th ...	2004	15528494
a dual-genome symbiosis chip for coordinate study of signal exchange and development in a prokaryote-host interaction.	the soil-dwelling alpha-proteobacterium sinorhizobium meliloti engages in a symbiosis with legumes: s. meliloti elicits the formation of plant root nodules where it converts dinitrogen to ammonia for use by the plant in exchange for plant photosynthate. to study the coordinate differentiation of s. meliloti and its legume partner during nodule development, we designed a custom affymetrix genechip with the complete s. meliloti genome and approximately 10,000 probe sets for the plant host, medicag ...	2004	15542588
katg is the primary detoxifier of hydrogen peroxide produced by aerobic metabolism in bradyrhizobium japonicum.	bacteria are exposed to reactive oxygen species from the environment and from those generated by aerobic metabolism. catalases are heme proteins that detoxify h(2)o(2), and many bacteria contain more than one catalase enzyme. also, the nonheme peroxidase alkyl hydroperoxide reductase (ahp) is the major scavenger of endogenous h(2)o(2) in escherichia coli. here, we show that aerobically grown bradyrhizobium japonicum cells express a single catalase activity. four genes encoding putative catalases ...	2004	15547258
the recombination genes addab are not restricted to gram-positive bacteria: genetic analysis of the recombination initiation enzymes recf and addab in rhizobium etli.	single-strand gaps (ssgs) and double-strand breaks (dsbs) are the major initiation sites for recombination. in bacteria, the ssgs are repaired by recfor, while the dsbs are processed by recbcd in gram-negative bacteria and addab in gram-positive bacteria. unexpectedly, instead of recbcd genes, the addab genes were found in members of the alpha-proteobacteria group (gram negative). taking rhizobium etli as a model, the role of recf and addab genes in homologous recombination and repair of damaged ...	2004	15547262
[the significance of exometabolites in the formation and operation of the soybean-rhizobium symbiosis].	the effect of various inoculates of the soybean-specific strain of nodule bacteria bradyrhizobium japonicum 634b (unwashed cells, cells washed from the exopolysaccharide-protein complex, and cells combined with the complex) on the formation and operation of soybean-rhizobium symbiosis. it was shown that addition of the exopolysaccharide-protein complex doubled the ability of the microsymbiont to form nodules, nodule weight, and the nitrogenase activity of the nodules. bradyrhizobium japonicum 63 ...	2004	15553789
rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer.	the enzyme porphobilinogen synthase (pbgs), which is central to the biosynthesis of heme, chlorophyll and cobalamins, has long been known to use a variety of metal ions and has recently been shown able to exist in two very different quaternary forms that are related to metal ion usage. this paper reports new information on the metal ion independence and quaternary structure of pbgs from the photosynthetic bacterium rhodobacter capsulatus.	2004	15555082
functional analysis of methylthioribose kinase genes in plants.	through a biochemical and a genetic approach, we have identified several plant genes encoding methylthioribose (mtr) kinase, an enzyme involved in recycling of methionine through the methylthioadenosine (mta) cycle. osmtk1, an mtr kinase from rice (oryza sativa), is 48.6 kd in size and shows cooperative kinetics with a v(max) of 4.9 pmol/min and a k0.5 of 16.8 microm. mtr kinase genes are the first genes to be identified from the mta cycle in plants. insertional mutagenesis of the unique atmtk g ...	2004	15557090
shear rate moderates community diversity in freshwater biofilms.	the development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. however, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. we hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. in order to study this hypothesis, freshwater biofilms were ...	2004	15574945
complete nucleotide sequence of the conjugative tetracycline resistance plasmid pfbaot6, a member of a group of incu plasmids with global ubiquity.	this study presents the first complete sequence of an incu plasmid, pfbaot6. this plasmid was originally isolated from a strain of aeromonas caviae from hospital effluent (westmorland general hospital, kendal, united kingdom) in september 1997 (g. rhodes, g. huys, j. swings, p. mcgann, m. hiney, p. smith, and r. w. pickup, appl. environ. microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pfbaot6 is 84,748 bp long and has 94 predicted coding sequences, ...	2004	15574953
new insights into type ii nad(p)h:quinone oxidoreductases.	type ii nad(p)h:quinone oxidoreductases (ndh-2) catalyze the two-electron transfer from nad(p)h to quinones, without any energy-transducing site. ndh-2 accomplish the turnover of nad(p)h, regenerating the nad(p)(+) pool, and may contribute to the generation of a membrane potential through complexes iii and iv. these enzymes are usually constituted by a nontransmembrane polypeptide chain of approximately 50 kda, containing a flavin moiety. there are a few compounds that can prevent their activity ...	2004	15590775
mitochondrial cytochrome c1 is a collapsed di-heme cytochrome.	cytochrome c(1) from mitochondrial complex iii and the di-heme cytochromes c in the corresponding enzyme from epsilon-proteobacteria have so far been considered to represent unrelated cytochromes. a missing link protein discovered in the genome of the hyperthermophilic bacterium aquifex aeolicus, however, provides evidence for a close evolutionary relationship between these two cytochromes. the mono-heme cytochrome c(1) from a. aeolicus contains stretches of strong sequence homology toward the e ...	2004	15591339
the elastic properties of the caulobacter crescentus adhesive holdfast are dependent on oligomers of n-acetylglucosamine.	the aquatic bacterium caulobacter crescentus attaches to solid surfaces through an adhesive holdfast located at the tip of its polar stalk, a thin cylindrical extension of the cell membrane. in this paper, the elastic properties of the c. crescentus stalk and holdfast assembly were studied by using video light microscopy. in particular, the contribution of oligomers of n-acetylglucosamine (glcnac) to the elasticity of holdfast was examined by lysozyme digestion. c. crescentus cells attached to a ...	2005	15601710
two heme binding sites are involved in the regulated degradation of the bacterial iron response regulator (irr) protein.	the iron response regulator (irr) protein from bradyrhizobium japonicum is a conditionally stable protein that degrades in response to cellular iron availability. this turnover is heme-dependent, and rapid degradation involves heme binding to a heme regulatory motif (hrm) of irr. here, we show that irr confers iron-dependent instability on glutathione s-transferase (gst) when fused to it. analysis of irr-gst derivatives with c-terminal truncations of irr implicated a second region necessary for ...	2004	15613477
the bldc developmental locus of streptomyces coelicolor encodes a member of a family of small dna-binding proteins related to the dna-binding domains of the merr family.	the bldc locus, required for formation of aerial hyphae in streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids d17 and d25 of a minimal ordered library. subcloning and sequencing showed that bldc encodes a member of a previously unrecognized family of small (58- to 78-residue) dna-binding proteins, related to the dna-binding domains of the merr family of transcriptional activators. bldc family members are found in a wide range of gram-positive and gram-nega ...	2005	15629942
identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal cys-loop ion channels.	acetylcholine receptor type ligand-gated ion channels (art-lgic; also known as cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, gaba, glutamate and histamine, and for zn2+ ions. they play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the metazoa.	2004	15642096
identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal cys-loop ion channels.	acetylcholine receptor type ligand-gated ion channels (art-lgic; also known as cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, gaba, glutamate and histamine, and for zn2+ ions. they play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the metazoa.	2004	15642096
pyruvate:quinone oxidoreductase from corynebacterium glutamicum: purification and biochemical characterization.	pyruvate:quinone oxidoreductase catalyzes the oxidative decarboxylation of pyruvate to acetate and co2 with a quinone as the physiological electron acceptor. so far, this enzyme activity has been found only in escherichia coli. using 2,6-dichloroindophenol as an artificial electron acceptor, we detected pyruvate:quinone oxidoreductase activity in cell extracts of the amino acid producer corynebacterium glutamicum. the activity was highest (0.055 +/- 0.005 u/mg of protein) in cells grown on compl ...	2005	15659664
heat shock proteome analysis of wild-type corynebacterium glutamicum atcc 13032 and a spontaneous mutant lacking groel1, a dispensable chaperone.	proteome analysis of corynebacterium glutamicum atcc 13032 showed that levels of several proteins increased drastically in response to heat shock. these proteins were identified as dnak, groel1, groel2, clpb, grpe, and poxb, and their heat response was in agreement with previous transcriptomic results. a major heat-induced protein was absent in the proteome of strain 13032b of c. glutamicum, used for genome sequencing in germany, compared with the wild-type atcc 13032 strain. the missing protein ...	2005	15659666
nopb, a type iii secreted protein of rhizobium sp. strain ngr234, is associated with pilus-like surface appendages.	rhizobium sp. strain ngr234 possesses a functional type three secretion system (ttss), through which a number of proteins, called nodulation outer proteins (nops), are delivered to the outside of the cell. a major constraint to the identification of nops is their low abundance in the supernatants of ngr234 strains grown in culture. to overcome this limitation, a more sensitive proteomics-based strategy was developed. secreted proteins from wild-type ngr234 were separated by two-dimensional gel e ...	2005	15659692
molecular characterization of uptake hydrogenase in frankia.	a molecular characterization of uptake hydrogenase in frankia was performed by using two-dimensional gel electrophoresis, matrix-assisted laser-desorption ionization-time-of-flight mass spectrometry, pcr amplification and southern blotting. a polypeptide of approx. 60 kda was recognized in frankia ugl011102, avci1 and kb5 on the two-dimensional gel by blotting with ralstonia eutropha (hox g) antibody. further analysis by ms resulted in a peptide 'fingerprint', which was similar to the membrane-b ...	2005	15667266
molybdate-dependent expression of the periplasmic nitrate reductase in bradyrhizobium japonicum.	the napedabc genes of bradyrhizobium japonicum encode the periplasmic nitrate reductase, an mo-containing enzyme which catalyses the reduction of nitrate to nitrite when oxygen concentrations are limiting. in this bacterium, another set of genes, modabc, code for a high affinity abc-type mo transport system. a b. japonicum moda mutant has been obtained that is not capable of growing anaerobically with nitrate and lacks nitrate reductase activity. under nitrate respiring conditions, when mo conce ...	2005	15667283
the complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium bradyrhizobium japonicum.	denitrification is an alternative form of respiration in which bacteria sequentially reduce nitrate or nitrite to nitrogen gas by the intermediates nitric oxide and nitrous oxide when oxygen concentrations are limiting. in bradyrhizobium japonicum, the n(2)-fixing microsymbiont of soya beans, denitrification depends on the napedabc, nirk, norcbqd, and nosrzdfylx gene clusters encoding nitrate-, nitrite-, nitric oxide- and nitrous oxide-reductase respectively. mutational analysis of the b. japoni ...	2005	15667287
one-component systems dominate signal transduction in prokaryotes.	two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. by analyzing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. one-component systems are evolutionarily older, more widely distributed among bacteria and archaea, ...	2005	15680762
mutational and biochemical analysis of cytochrome c', a nitric oxide-binding lipoprotein important for adaptation of neisseria gonorrhoeae to oxygen-limited growth.	neisseria gonorrhoeae is a prolific source of c-type cytochromes. five of the constitutively expressed cytochromes are predicted, based on in silico analysis of the n. gonorrhoeae genome, to be components of the cytochrome bc1 complex, cytochrome c oxidase cbb3 or periplasmic cytochromes involved in electron transfer reactions typical of a bacterium with a microaerobic physiology. cytochrome c peroxidase was previously shown to be a lipoprotein expressed only during oxygen-limited growth. the fi ...	2005	15689189
novel avidin-like protein from a root nodule symbiotic bacterium, bradyrhizobium japonicum.	bradyrhizobium japonicum is an important nitrogenfixing symbiotic bacterium, which can form root nodules on soybeans. these bacteria have a gene encoding a putative avidin- and streptavidin-like protein, which bears an amino acid sequence identity of only about 30% over the core regions with both of them. we produced this protein in escherichia coli both as the full-length wild type and as a c-terminally truncated core form and showed that it is indeed a high affinity biotin-binding protein that ...	2005	15695809
role of arginine 220 in the oxygen sensor fixl from bradyrhizobium japonicum.	in the heme-based oxygen sensor protein fixl, conformational changes induced by oxygen binding to the heme sensor domain regulate the activity of a neighboring histidine kinase, eventually restricting expression of specific genes to hypoxic conditions. the conserved arginine 220 residue is suggested to play a key role in the signal transduction mechanism. to obtain detailed insights into the role of this residue, we replaced arg(220) by histidine (r220h), glutamine (r220q), glutamate (r220e), an ...	2005	15711013
protein domains and architectural innovation in plant-associated proteobacteria.	evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...	2005	15715905
insights into the domains required for dimerization and assembly of human alphab crystallin.	protein pin array technology was used to identify subunit-subunit interaction sites in the small heat shock protein (shsp) alphab crystallin. subunit-subunit interaction sites were defined as consensus sequences that interacted with both human alphaa crystallin and alphab crystallin. the human alphab crystallin protein pin array consisted of contiguous and overlapping peptides, eight amino acids in length, immobilized on pins that were in a 96-well elisa plate format. the interaction of alphab c ...	2005	15722445
genomic characterization of non-o1, non-o139 vibrio cholerae reveals genes for a type iii secretion system.	non-o1, non-o139 vibrio cholerae can cause gastroenteritis and extraintestinal infections, but, unlike o1 and o139 strains of v. cholerae, little is known about the virulence gene content of non-o1, non-o139 strains and their phylogenetic relationship to other pathogenic v. cholerae. comparative genomic microarray analysis of four pathogenic non-o1, non-o139 strains indicates that these strains are quite divergent from o1 and o139 strains. genomic sequence analysis of a non-o1, non-o139 strain ( ...	2005	15728357
variation in the strength of selected codon usage bias among bacteria.	among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. however, in other species selection appears to have been ineffective. here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. the approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. the ...	2005	15728743
transcriptional control of the rhuir-bhurstuv heme acquisition locus in bordetella avium.	iron (fe) is an essential nutrient for most bacterial pathogens. in these organisms, a variety of regulatory systems that respond to specific fe complexes found within their vertebrate hosts have evolved. in bordetella avium, the heme utilization locus encoded by rhuir-bhurstuv mediates efficient acquisition of fe from heme and hemoproteins. control of bhurstuv expression is promulgated at two levels. when fe is abundant, expression is repressed in a fur-dependent manner which is partially relie ...	2005	15731061
a multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and expression in vivo.	we have constructed a novel tetra-promoter vector (pbvboostfg) system that enables screening of gene/cdna libraries for functional genomic studies. the vector enables an all-in-one strategy for gene expression in mammalian, bacterial and insect cells and is also suitable for direct use in vivo. virus preparation is based on an improved mini tn7 transpositional system allowing easy and fast production of recombinant baculoviruses with high diversity and negligible background. cloning of the desir ...	2005	15731335
functional domains of nosr, a novel transmembrane iron-sulfur flavoprotein necessary for nitrous oxide respiration.	bacterial nitrous oxide (n2o) respiration depends on the polytopic membrane protein nosr for the expression of n2o reductase from the nosz gene. we constructed his-tagged nosr and purified it from detergent-solubilized membranes of pseudomonas stutzeri atcc 14405. nosr is an iron-sulfur flavoprotein with redox centers positioned at opposite sides of the cytoplasmic membrane. the flavin cofactor is presumably bound covalently to an invariant threonine residue of the periplasmic domain. nosr also ...	2005	15743947
nodulation of lupinus albus by strains of ochrobactrum lupini sp. nov.	the nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the alpha-proteobacteria. however, in the last 3 years four nonrhizobial species, belonging to alpha and beta subclasses of the proteobacteria, have been described as legume-nodulating bacteria. in the present study, two fast-growing strains, lup21 and lup23, were isolated from nodules of lupinus honoratus. the phylogenetic analysis ...	2005	15746334
genomic analysis of bacteriophage phijl001: insights into its interaction with a sponge-associated alpha-proteobacterium.	bacteriophage phijl001 infects a novel marine bacterium in the alpha subclass of the proteobacteria isolated from the marine sponge ircinia strobilina. phijl001 is a siphovirus and forms turbid plaques on its host. the genome sequence of phijl001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. the complete genome sequence of phijl001 comprised 63,469 bp with an overall g+c content of 62%. the genome has 91 predicted ...	2005	15746365
the acetate switch.	to succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. one such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. this review explains why, when, and how cells excrete or dissimilate acetate. the central components of the "switch" (phos ...	2005	15755952
detection of and response to signals involved in host-microbe interactions by plant-associated bacteria.	diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. this concept was first demonstrated for the members of the family rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and anima ...	2005	15755957
a comprehensive update of the sequence and structure classification of kinases.	a comprehensive update of the classification of all available kinases was carried out. this survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme.	2005	15771780
bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (papilionoideae: genisteae) from the canary islands, along with bradyrhizobium japonicum bv. genistearum, bradyrhizobium genospecies alpha and bradyrhizobium genospecies beta.	highly diverse bradyrhizobium strains nodulate genistoid legumes (brooms) in the canary islands, morocco, spain and the americas. phylogenetic analyses of its, atpd, glnii and reca sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely bradyrhizobium japonicum and three unnamed genospecies. dna-dna hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name bradyrhizobium canarien ...	2005	15774626
rna interference of soybean isoflavone synthase genes leads to silencing in tissues distal to the transformation site and to enhanced susceptibility to phytophthora sojae.	isoflavones are thought to play diverse roles in plant-microbe interactions and are also potentially important to human nutrition and medicine. isoflavone synthase (ifs) is a key enzyme for the formation of the isoflavones. here, we examined the consequences of rnai silencing of genes for this enzyme in soybean (glycine max). soybean cotyledon tissues were transformed with agrobacterium rhizogenes carrying an rnai silencing construct designed to silence expression of both copies of ifs genes. ap ...	2005	15778457
overlaps in the transcriptional profiles of medicago truncatula roots inoculated with two different glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza.	arbuscular mycorrhiza (am) is a widespread symbiotic association between plants and fungal microsymbionts that supports plant development under nutrient-limiting and various stress conditions. in this study, we focused on the overlapping genetic program activated by two commonly studied microsymbionts in addition to identifying am-related genes. we thus applied 16,086 probe microarrays to profile the transcriptome of the model legume medicago truncatula during interactions with glomus mosseae an ...	2005	15778460
tissue-specific localization of pea root infection by nectria haematococca. mechanisms and consequences.	root infection in susceptible host species is initiated predominantly in the zone of elongation, whereas the remainder of the root is resistant. nectria haematococca infection of pea (pisum sativum) was used as a model to explore possible mechanisms influencing the localization of root infection. the failure to infect the root tip was not due to a failure to induce spore germination at this site, suppression of pathogenicity genes in the fungus, or increased expression of plant defense genes. in ...	2005	15778461
inhibition of n2 fixation in soybean is associated with elevated ureides and amino acids.	decreased n2 fixation in soybean (glycine max) l. merr. during water deficits has been associated with increases in ureides and free amino acids in plant tissues, indicating a potential feedback inhibition by these compounds in response to drought. we evaluated concentrations of ureides and amino acids in leaf and nodule tissue and the concurrent change in n2 fixation in response to exogenous ureides and soil-water treatments for the cultivars jackson and ks4895. exogenous ureides applied to the ...	2005	15778462
partial reconstruction of flavonoid and isoflavonoid biosynthesis in yeast using soybean type i and type ii chalcone isomerases.	flavonoids and isoflavonoids are major plant secondary metabolites that mediate diverse biological functions and exert significant ecological impacts. these compounds play important roles in many essential physiological processes. in addition, flavonoids and isoflavonoids have direct but complex effects on human health, ranging from reducing cholesterol levels and preventing certain cancers to improving women's health. in this study, we cloned and functionally characterized five soybean (glycine ...	2005	15778463
alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome p450 encoded on the nifd excision element of anabaena 7120.	alkanes have been hypothesized to act as universal inducers of bacterial cytochrome p450 gene expression. we tested this hypothesis on an unusual p450 gene (cyp110) found on a conserved 11 kilobase episomal dna element of unknown function found in filamentous cyanobacteria. we also monitored the binding of potential substrates to the p450 protein and explored the distribution of p450 protein in vegetative cells and nitrogen-fixing heterocysts using immuno-electron microscopy.	2005	15790415
transgenic expression of the soybean apyrase in lotus japonicus enhances nodulation.	the soybean apyrase, gs52, was previously characterized as an early nodulin that is expressed in roots and localized to the plasma membrane. transgenic lotus japonicus plants were constructed constitutively expressing the gs52 apyrase. segregation and southern-blot analysis identified four single-copy sense lines, several double-copy sense lines, and one double-copy antisense line for further analysis. the single- and double-copy sense gs52 l. japonicus lines had enhanced nodulation that correla ...	2005	15793071
gmn70 and ljn70. anion transporters of the symbiosome membrane of nodules with a transport preference for nitrate.	a cdna was isolated from soybean (glycine max) nodules that encodes a putative transporter (gmn70) of the major facilitator superfamily. gmn70 is expressed predominantly in mature nitrogen-fixing root nodules. by western-blot and immunocytochemical analyses, gmn70 was localized to the symbiosome membrane of infected root nodule cells, suggesting a transport role in symbiosis. to investigate its transport function, crna encoding gmn70 was expressed in xenopus laevis oocytes, and two-electrode vol ...	2005	15793072
systematic association of genes to phenotypes by genome and literature mining.	one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ...	2005	15799710
the histidine of the c-type cytochrome cxxch haem-binding motif is essential for haem attachment by the escherichia coli cytochrome c maturation (ccm) apparatus.	c-type cytochromes are characterized by covalent attachment of haem to the protein by two thioether bonds formed between the haem vinyl groups and the cysteine sulphurs in a cxxch peptide motif. in escherichia coli and many other gram-negative bacteria, this post-translational haem attachment is catalysed by the ccm (cytochrome c maturation) system. the features of the apocytochrome substrate required and recognized by the ccm apparatus are uncertain. in the present study, we report investigatio ...	2005	15801911
functional insights from the distribution and role of homopeptide repeat-containing proteins.	expansion of "low complex" repeats of amino acids such as glutamine (poly-q) is associated with protein misfolding and the development of degenerative diseases such as huntington's disease. the mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (rcps) remains obscure, and the role (if any) of repeat regions remains to be determined. here, a web-accessible database of rcps is presented. the distribution and evolution of rcps t ...	2005	15805494
insights into heme-based o2 sensing from structure-function relationships in the fixl proteins.	fixl proteins are bacterial heme-containing signal transduction proteins responsible for sensing the o(2) concentration in the organism's environment. in sinorhizobium meliloti fixl is a protein histidine kinase that, together with its response regulator fixj, constitute an oxygen-sensitive switch for regulation of the organism's nitrogen fixation and microaerobic respiration genes. the o(2) sensitivity of the switch is such that it transitions during the process of symbiosis in alfalfa roots. b ...	2005	15811514
6s rna is a widespread regulator of eubacterial rna polymerase that resembles an open promoter.	6s rna is an abundant noncoding rna in escherichia coli that binds to sigma70 rna polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. we have computationally identified >100 new 6s rna homologs in diverse eubacterial lineages. two abundant bacillus subtilis rnas of unknown function (bsra and bsrb) and cyanobacterial 6sa rnas are now recognized as 6s homologs. structural probing of e. coli 6s rna and a b. subtilis homolo ...	2005	15811922
biocatalytic production of perillyl alcohol from limonene by using a novel mycobacterium sp. cytochrome p450 alkane hydroxylase expressed in pseudomonas putida.	a number of oxygenated monoterpenes present at low concentrations in plant oils have anticarcinogenic properties. one of the most promising compounds in this respect is (-)-perillyl alcohol. since this natural product is present only at low levels in a few plant oils, an alternative, synthetic source is desirable. screening of 1,800 bacterial strains showed that many alkane degraders were able to specifically hydroxylate l-limonene in the 7 position to produce enantiopure (-)-perillyl alcohol. t ...	2005	15811996
cloning, expression, and site-directed mutagenesis of the propene monooxygenase genes from mycobacterium sp. strain m156.	propene monooxygenase has been cloned from mycobacterium sp. strain m156, based on hybridization with the amoabcd genes of rhodococcus corallinus b276. sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that from r. corallinus b-276. attempts were made to express the pmoabcd operon in escherichia coli and mycobacterium smegmatis mc(2)155. in the former, there appeared to be a proble ...	2005	15812019
improved assessment of denitrifying, n2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes.	a database of terminal restriction fragments (trfs) of the 16s rrna gene was set up utilizing 13 restriction enzymes and 17,327 genbank sequences. a computer program, termed trefid, was developed to allow identification of any of these 17,327 sequences by means of polygons generated from the specific trfs of each bacterium. the trefid program complements and exceeds in its data content the web-based phylogenetic assignment tool recently described by a. d. kent, d. j. smith, b. j. benson, and e. ...	2005	15812035
isolation and characterization of feca- and feob-mediated iron acquisition systems of the spirochete leptospira biflexa by random insertional mutagenesis.	the specific mechanisms by which leptospira spp. acquire iron from their ecological niches are unknown. a major factor contributing to our ignorance of spirochetal biology is the lack of methods for genetic analysis of these organisms. in this study, we have developed a system for random transposon mutagenesis of leptospira biflexa using a mariner transposon, himar1. to demonstrate the validity of himar1 in vivo transposon mutagenesis in l. biflexa, a screen of mutants for clones impaired in ami ...	2005	15838052
transcription activation in vitro by the bradyrhizobium japonicum regulatory protein fixk2.	in bradyrhizobium japonicum, the n2-fixing root nodule endosymbiont of soybean, a group of genes required for microaerobic, anaerobic, or symbiotic growth is controlled by fixk2, a key regulator that is part of the fixlj-fixk2 cascade. fixk2 belongs to the family of cyclic amp receptor protein/fumarate and nitrate reductase (crp/fnr) transcription factors that recognize a palindromic dna motif (crp/fnr box) associated with the regulated promoters. here, we report on a biochemical analysis of fix ...	2005	15866917
an adenylyl cyclase, cyab, acts as an osmosensor in myxococcus xanthus.	we have previously reported that a receptor-type adenylyl cyclase (cyaa) of myxococcus xanthus undergoes an osmosensor mainly during spore germination (y. kimura et al., j. bacteriol. 184:3578-3585, 2002). in the present study, we cloned another receptor-type adenylyl cyclase gene (cyab) and characterized the function of the cyab-encoded protein. disruption of cyab generates a mutant that showed growth retardation at high ionic (nacl) or high nonionic (sucrose) osmolarity. when vegetative cells ...	2005	15866951
utilization of the plant hormone indole-3-acetic acid for growth by pseudomonas putida strain 1290.	we have isolated from plant surfaces several bacteria with the ability to catabolize indole-3-acetic acid (iaa). one of them, isolate 1290, was able to utilize iaa as a sole source of carbon, nitrogen, and energy. the strain was identified by its 16s rrna sequence as pseudomonas putida. activity of the enzyme catechol 1,2-dioxygenase was induced during growth on iaa, suggesting that catechol is an intermediate of the iaa catabolic pathway. this was in agreement with the observation that the oxyg ...	2005	15870323
an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus.	dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ...	2005	15886391
diverse bacteria isolated from root nodules of phaseolus vulgaris and species within the genera campylotropis and cassia grown in china.	eighty bacterial isolates from root nodules of the leguminous plants phaseolus vulgaris, campylotropis spp. and cassia spp. grown in china were classified into five groups by phenotypic analyses, sds-page of whole-cell proteins, pcr-based 16s rrna gene restriction-fragment-length-polymorphism and sequencing. thirty-three isolates from the three plant genera were identified as agrobacterium tumefaciens because they are closely related to the type strain of a. tumefaciens. fourteen isolates from p ...	2005	15900972
purification and characterization of allophanate hydrolase (atzf) from pseudomonas sp. strain adp.	atzf, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. in the present study, the atzf gene from pseudomonas sp. strain adp was cloned and expressed as a his-tagged protein, and the protein was purified and characterized. atzf had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. the acti ...	2005	15901697
identification of a turnover element in region 2.1 of escherichia coli sigma32 by a bacterial one-hybrid approach.	induction of the heat shock response in escherichia coli requires the alternative sigma factor sigma32 (rpoh). the cellular concentration of sigma32 is controlled by proteolysis involving ftsh, other proteases, and the dnakj chaperone system. to identify individual sigma32 residues critical for degradation, we used a recently developed bacterial one-hybrid system and screened for stabilized versions of sigma32. the five single point mutations that rendered the sigma factor more stable mapped to ...	2005	15901705
prediction of functional modules based on comparative genome analysis and gene ontology application.	we present a computational method for the prediction of functional modules encoded in microbial genomes. in this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. we first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and gene ontology ass ...	2005	15901854
evaluation of the role of genes encoding for dehydrin proteins (lea d-11) during drought stress in arbuscular mycorrhizal glycine max and lactuca sativa plants.	in this study, it has been determined whether the arbuscular mycorrhizal (am) symbiosis is able to alter the pattern of dehydrin (lea d-11 group) transcript accumulation under drought stress, and whether such a possible alteration functions in the protection of the host plants against drought. two dehydrin-encoding genes have been cloned from glycine max (gmlea 8 and gmlea 10) and one from lactuca sativa (lslea 1) and they have been analysed for their contribution to the response against drought ...	2005	15911559
conserved modular design of an oxygen sensory/signaling network with species-specific output.	principles of modular design are evident in signaling networks that detect and integrate a given signal and, depending on the organism in which the network module is present, transduce this signal to affect different metabolic or developmental pathways. here we report a global transcriptional analysis of an oxygen sensory/signaling network in caulobacter crescentus consisting of the sensor histidine kinase fixl, its cognate response regulator fixj, the transcriptional regulator fixk, and the kin ...	2005	15911751
proteomic analysis of soybean root hairs after infection by bradyrhizobium japonicum.	infection of soybean root hairs by bradyrhizobium japonicum is the first of several complex events leading to nodulation. in the current proteomic study, soybean root hairs after inoculation with b. japonicum were separated from roots. total proteins were analyzed by two-dimensional (2-d) polyacrylamide gel electrophoresis. in one experiment, 96 protein spots were analyzed by matrix-assisted laser desorption ionization time-of-flight (maldi-tof) mass spectrometry (ms) to compare protein profiles ...	2005	15915644
effect of chlorimuron-ethyl on bradyrhizobium japonicum and its symbiosis with soybean.	possible side-effects of the acetolactate synthase (als)-inhibiting herbicide chlorimuron-ethyl on bradyrhizobium japonicum (kirchner & jordan) in pure culture and on inoculated soybean plants growing under controlled conditions were investigated. growth of b japonicum strain e109 was not affected by this herbicide even when exposed to concentrations 150 times higher than recommended field doses. however, nodulation of soybean plants treated 5 days after emergence with chlorimuron-ethyl at stand ...	2005	15920784
automatic selection of representative proteins for bacterial phylogeny.	although there are now about 200 complete bacterial genomes in genbank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence.	2005	15927057
identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph acidithiobacillus ferrooxidans.	a cluster of five genes, proposed to be involved in the formation of extracellular polysaccharide (eps) precursors via the leloir pathway, have been identified in the acidophilic autotroph acidithiobacillus ferrooxidans. the order of the genes is luxa-gale-galk-pgm-galm, encoding a luxa-like protein, udp-glucose 4-epimerase, galactokinase, phosphoglucomutase, and galactose mutarotase, respectively. the gal cluster forms a single transcriptional unit and is therefore an operon. two other putative ...	2005	15932984
mutations in cytochrome assembly and periplasmic redox pathways in bordetella pertussis.	transposon mutagenesis of bordetella pertussis was used to discover mutations in the cytochrome c biogenesis pathway called system ii. using a tetramethyl-p-phenylenediamine cytochrome c oxidase screen, 27 oxidase-negative mutants were isolated and characterized. nine mutants were still able to synthesize c-type cytochromes and possessed insertions in the genes for cytochrome c oxidase subunits (ctac, -d, and -e), heme a biosynthesis (ctab), assembly of cytochrome c oxidase (sco2), or ferrochela ...	2005	15937156
identification of the omega4406 regulatory region, a developmental promoter of myxococcus xanthus, and a dna segment responsible for chromosomal position-dependent inhibition of gene expression.	when starved, myxococcus xanthus cells send signals to each other that coordinate their movements, gene expression, and differentiation. c-signaling requires cell-cell contact, and increasing contact brought about by cell alignment in aggregates is thought to increase c-signaling, which induces expression of many genes, causing rod-shaped cells to differentiate into spherical spores. c-signaling involves the product of the csga gene. a csga mutant fails to express many genes that are normally in ...	2005	15937177
recombinant pas-heme domains of oxygen sensing proteins: high level production and physical characterization.	details of a high-level recombinant production method for the heme-pas domains of heme oxygen sensing proteins from sinorhizobium meliloti (sm) (formerly rhizobium meliloti, rm), bradyrhizobium japonicum (bj), and escherichia coli (ec) are described. using a newly proposed, concise, and unambiguous naming system (also described here) these proteins are: smfixlh(128-264), bjfixlh(140-270), and ecdosh(1-147). in addition, high-level production of bjfixl(140-505), the soluble full-length protein co ...	2005	15939306
unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression.	a major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. in vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. the widely used gene-to-phenotype approach involves the identification of altered niche-related phen ...	2005	15944455
the tetr family of transcriptional repressors.	we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ...	2005	15944459
a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts.	analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.	2005	15955239
signature proteins that are distinctive of alpha proteobacteria.	the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group.	2005	15960851
the net of life: reconstructing the microbial phylogenetic network.	it has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (hgt) events. yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. here, we present a first attempt to reconstruct such an evolutionary network, which we term the "net of life". we use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference alg ...	2005	15965028
the pleiotropic nature of symbiotic regulatory mutants: bradyrhizobium japonicum nifa gene is involved in control of nif gene expression and formation of determinate symbiosis.	in the slow-growing soybean symbiont, bradyrhizobium japonicum (strain 110), a nifa-like regulatory gene was located immediately upstream of the previously mapped fixa gene. by interspecies hybridization and partial dna sequencing the gene was found to be homologous to nifa from klebsiella pneumoniae and rhizobium meliloti, and to a lesser extent, also to ntrc from k. pneumoniae. the b. japonicum nifa gene product was shown to activate b. japonicum and k. pneumoniae nif promoters (using nif::lac ...	1986	15966104
characterization of a bifunctional puta homologue from bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor.	puta is a bifunctional flavoenzyme in bacteria that catalyzes the four-electron oxidation of proline to glutamate. in certain prokaryotes such as escherichia coli, puta is also a transcriptional repressor of the proline utilization (put) genes and thus is trifunctional. in this work, we have begun to assess differences between bifunctional and trifunctional puta enzymes by examining the puta protein from bradyrhizobium japonicum (bjputa). primary structure analysis of bjputa shows it lacks the d ...	2005	15966737