| gene fusions and gene duplications: relevance to genomic annotation and functional analysis. | escherichia coli a model organism provides information for annotation of other genomes. our analysis of its genome has shown that proteins encoded by fused genes need special attention. such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. previous work overstated the number of multimodular proteins in e. coli. this work corrects ... | 2005 | 15757509 |
| bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion. | like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ... | 2005 | 15757514 |
| the capsular polysaccharide biosynthesis of streptococcus pneumoniae serotype 8: functional identification of the glycosyltransferase wcis (cap8h). | cps (capsular polysaccharide) is a major virulence factor in streptococcus pneumoniae. biosynthesis of cps ru (repeat unit) proceeds by sequential transfer of sugar residues from the appropriate sugar donor to an activated lipid carrier by committed gts (glycosyltransferases). while the nucleotide sequence of many cps loci is already known, the real substrate specificity of the hypothetical gts, as well as the sequence of sugar addition is unclear. in the present paper, we report the biochemical ... | 2005 | 15766331 |
| importance of unusually modified lipid a in sinorhizobium stress resistance and legume symbiosis. | sinorhizobium meliloti, a legume symbiont and brucella abortus, a phylogenetically related mammalian pathogen, both require their baca proteins to establish chronic intracellular infections in their respective hosts. the lipid a molecules of s. meliloti and b. abortus are unusually modified with a very-long-chain fatty acid (vlcfa; c > or = 28) and we discovered that baca is involved in this unusual modification. this observation raised the possibility that the unusual lipid a modification could ... | 2005 | 15773979 |
| identification of new protein-protein interactions involving the products of the chromosome- and plasmid-encoded type iv secretion loci of the phytopathogen xanthomonas axonopodis pv. citri. | the recently sequenced genome of the bacterial plant pathogen xanthomonas axonopodis pv. citri contains two virb gene clusters, one on the chromosome and one on a 64-kb plasmid, each of which codes for a previously uncharacterized type iv secretion system (t4ss). here we used a yeast two-hybrid assay to identify protein-protein interactions in these two systems. our results revealed interactions between known t4ss components as well as previously uncharacterized interactions involving hypothetic ... | 2005 | 15774874 |
| identification of cohesive ends and genes encoding the terminase of phage 16-3. | cohesive ends of 16-3, a temperate phage of rhizobium meliloti 41, have been identified as 10-base-long, 3'-protruding complementary g/c-rich sequences. ters and terl encode the two subunits of 16-3 terminase. significant homologies were detected among the terminase subunits of phage 16-3 and other phages from various ecosystems. | 2005 | 15774897 |
| invasion of lotus japonicus root hairless 1 by mesorhizobium loti involves the nodulation factor-dependent induction of root hairs. | in many legumes, including lotus japonicus and medicago truncatula, susceptible root hairs are the primary sites for the initial signal perception and physical contact between the host plant and the compatible nitrogen-fixing bacteria that leads to the initiation of root invasion and nodule organogenesis. however, diverse mechanisms of nodulation have been described in a variety of legume species that do not rely on root hairs. to clarify the significance of root hairs during the l. japonicus-me ... | 2005 | 15778455 |
| 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 |
| construction of a mini-tn5-luxcdabe mutant library in pseudomonas aeruginosa pao1: a tool for identifying differentially regulated genes. | pseudomonas aeruginosa is a major cause of nosocomial (hospital-derived) infections, is the predominant pathogen in chronic cystic fibrosis lung infections, and remains difficult to treat due to its high intrinsic antibiotic resistance. the completion of the p. aeruginosa pao1 genome sequence provides the opportunity for genome-wide studies to increase our understanding of the pathogenesis and biology of this important pathogen. in this report, we describe the construction of a mini-tn5-luxcdabe ... | 2005 | 15805499 |
| nifh promoter activity is regulated by dna supercoiling in sinorhizobium meliloti. | in prokaryotes, dna supercoiling regulates the expression of many genes; for example, the expression of klebsiella pneumoniae nifla operon depends on dna negative supercoiling in anaerobically grown cells, which indicates that dna supercoiling might play a role in gene regulation of the anaerobic response. since the expression of the nifh promoter in sinorhizobium meliloti is not repressed by oxygen, it is proposed that the status of dna supercoiling may not affect the expression of the nifh pro ... | 2005 | 15806287 |
| automated metabolic reconstruction for methanococcus jannaschii. | we present the computational prediction and synthesis of the metabolic pathways in methanococcus jannaschii from its genomic sequence using the pathologic software. metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. we predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. these assignments r ... | 2004 | 15810431 |
| automated metabolic reconstruction for methanococcus jannaschii. | we present the computational prediction and synthesis of the metabolic pathways in methanococcus jannaschii from its genomic sequence using the pathologic software. metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. we predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. these assignments r ... | 2004 | 15810431 |
| 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 |
| azospirillum brasilense produces the auxin-like phenylacetic acid by using the key enzyme for indole-3-acetic acid biosynthesis. | an antimicrobial compound was isolated from azospirillum brasilense culture extracts by high-performance liquid chromatography and further identified by gas chromatography-mass spectrometry as the auxin-like molecule, phenylacetic acid (paa). paa synthesis was found to be mediated by the indole-3-pyruvate decarboxylase, previously identified as a key enzyme in indole-3-acetic acid (iaa) production in a. brasilense. in minimal growth medium, paa biosynthesis by a. brasilense was only observed in ... | 2005 | 15812004 |
| dispersal and evolution of the sinorhizobium meliloti group ii rmint1 intron in bacteria that interact with plants. | group ii introns are both self-splicing rnas and mobile retroelements found in bacterial and archaeal genomes and in organelles of eukaryotes. they are thought to be the ancestors of eukaryote spliceosomal introns and non-long terminal repeat retrotransposons. we show here that rmint1, a bacterial group ii intron first described in the nitrogen-fixing symbiont of alfalfa (medicago sativa) sinorhizobium meliloti, is also present in other sinorhizobium and rhizobium species. the intron-homing site ... | 2005 | 15814827 |
| biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from sphingomonas sp. strain 113p3. | oxidized polyvinyl alcohol hydrolase (oph) and polyvinyl alcohol dehydrogenase were found to be constitutively present in the periplasm of sphingomonas sp. strain 113p3 (formerly pseudomonas sp. 113p3). the oph was purified to homogeneity with a yield of 40 % and a 5.9-fold increase in specific activity. the enzyme was a homodimer consisting of 35 kda subunits. its activity was inhibited by pmsf, hg(2+) and zn(2+). the enzyme hydrolysed oxidized polyvinyl alcohol (oxidized pva) and p-nitrophenyl ... | 2005 | 15817792 |
| control of speed modulation (chemokinesis) in the unidirectional rotary motor of sinorhizobium meliloti. | swimming cells of sinorhizobium meliloti are driven by flagella that rotate only clockwise. they can modulate rotary speed (achieve chemokinesis) and reorient the swimming path by slowing flagellar rotation. the flagellar motor is energized by proton motive force, and torque is generated by electrostatic interactions at the rotor/stator (flig/mota-motb) interface. like the escherichia coli flagellar motor that switches between counterclockwise and clockwise rotation, the s. meliloti rotary motor ... | 2005 | 15819626 |
| grafting between model legumes demonstrates roles for roots and shoots in determining nodule type and host/rhizobia specificity. | previous grafting experiments have demonstrated that legume shoots play a critical role in symbiotic development of nitrogen-fixing root nodules by regulating nodule number. here, reciprocal grafting experiments between the model legumes lotus japonicus and medicago truncatula were carried out to investigate the role of the shoot in the host-specificity of legume-rhizobia symbiosis and nodule type. lotus japonicus is nodulated by mesorhizobium loti and makes determinate nodules, whereas m. trunc ... | 2005 | 15824071 |
| phosphorylation-independent activity of atypical response regulators of helicobacter pylori. | the genome of the gastric pathogen helicobacter pylori harbors a remarkably low number of regulatory genes, including three and five open reading frames encoding two-component histidine kinases and response regulators, respectively, which are putatively involved in transcriptional regulation. two of the response regulator genes, hp1043 and hp166, proved to be essential for cell growth, and inactivation of the response regulator gene hp1021 resulted in a severe growth defect, as indicated by a sm ... | 2005 | 15838037 |
| molecular determinants for pspa-mediated repression of the aaa transcriptional activator pspf. | the escherichia coli phage shock protein system (pspabcde operon and pspg gene) is induced by numerous stresses related to the membrane integrity state. transcription of the psp genes requires the rna polymerase containing the sigma(54) subunit and the aaa transcriptional activator pspf. pspf belongs to an atypical class of sigma(54) aaa activators in that it lacks an n-terminal regulatory domain and is instead negatively regulated by another regulatory protein, pspa. pspa therefore represses it ... | 2005 | 15838051 |
| requirement of the receiver and phosphotransfer domains of arcb for efficient dephosphorylation of phosphorylated arca in vivo. | the arc two-component system, comprising the arcb sensor kinase and the arca response regulator, modulates the expression of numerous genes in response to the respiratory conditions of growth. under anoxic growth conditions, arcb autophosphorylates and transphosphorylates arca, which in turn represses or activates its target operons. under aerobic growth conditions, phosphorylated arca (arca-p) dephosphorylates and its transcriptional regulation is released. the dephosphorylation of arca-p has b ... | 2005 | 15838055 |
| a transcriptional response to singlet oxygen, a toxic byproduct of photosynthesis. | the ability of phototrophs to convert light into biological energy is critical for life on earth. however, there can be deleterious consequences associated with this bioenergetic conversion, including the production of toxic byproducts. for example, singlet oxygen (1o2) can be formed during photosynthesis by energy transfer from excited triplet-state chlorophyll pigments to o2. by monitoring gene expression and growth in the presence of 1o2, we show that the phototrophic bacterium rhodobacter sp ... | 2005 | 15855269 |
| cloning and characterization of a chromosomal class c beta-lactamase and its regulatory gene in laribacter hongkongensis. | laribacter hongkongensis, a newly discovered bacterium recently shown to be associated with community-acquired gastroenteritis, is generally resistant to most beta-lactams except the carbapenems. we describe the cloning and characterization of a novel chromosomal class c beta-lactamase and its regulatory gene in l. hongkongensis. two genes, ampc and ampr, were cloned by inserting restriction fragments of genomic dna from l. hongkongensis strain hlhk5 into pbk-cmv to give the recombinant plasmid ... | 2005 | 15855519 |
| microtubule dynamics in living root hairs: transient slowing by lipochitin oligosaccharide nodulation signals. | the incorporation of a fusion of green fluorescent protein and tubulin-alpha 6 from arabidopsis thaliana in root hairs of lotus japonicus has allowed us to visualize and quantify the dynamic parameters of the cortical microtubules in living root hairs. analysis of individual microtubule turnover in real time showed that only plus polymer ends contributed to overall microtubule dynamicity, exhibiting dynamic instability as the main type of microtubule behavior in lotus root hairs. comparison of t ... | 2005 | 15863517 |
| 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 |
| nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. | since operons are unstable across prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. thus, genes belonging to a given operon in one genome might re-associate in other genomes revealing functional relationships among gene products. we developed a system to build networks of functional relationships of gene products based on their organization into operons in any available genome. the operon predictions are based on inter-genic distances. our system can use d ... | 2005 | 15867197 |
| quantitative analysis of group ii intron expression and splicing in lactococcus lactis. | the group ii intron ll.ltrb is found within the ltrb relaxase gene of the conjugative element prs01 in lactococcus lactis. precise splicing of the intron is essential for prs01 transfer. the transcription regulation and in vivo splicing activity of ll.ltrb have not been investigated thoroughly in l. lactis in the natural prs01 context. we developed absolute quantitative real-time reverse transcription-pcr assays to quantify rna levels of the 5' exon (ltrbe1) and the spliced relaxase (ltrb) and i ... | 2005 | 15870348 |
| polychlorinated biphenyl rhizoremediation by pseudomonas fluorescens f113 derivatives, using a sinorhizobium meliloti nod system to drive bph gene expression. | rhizoremediation of organic chemicals requires high-level expression of biodegradation genes in bacterial strains that are excellent rhizosphere colonizers. pseudomonas fluorescens f113 is a biocontrol strain that was shown to be an excellent colonizer of numerous plant rhizospheres, including alfalfa. although a derivative of f113 expressing polychlorinated biphenyl (pcb) biodegradation genes (f113pcb) has been reported previously, this strain shows a low level of bph gene expression, limiting ... | 2005 | 15870360 |
| modulating dna bending affects nodd-mediated transcriptional control in rhizobium leguminosarum. | rhizobium leguminosarum nodd binds to the nod box of the inducible nod gene noda as a v-shaped tetramer and bends the nod box. in this work, we show that the nod gene inducer naringenin decreased gel mobility of nod box dna-nodd complexes by sharpening the nodd-induced dna bend, which correlated with noda transcription activation. nodd can induce different dna bends when the distance between the two half-sites of the nod box was modified, which severely affected nodd-mediated transcriptional con ... | 2005 | 15872217 |
| structural analysis and solution studies of the activated regulatory domain of the response regulator arca: a symmetric dimer mediated by the alpha4-beta5-alpha5 face. | escherichia coli react to changes from aerobic to anaerobic conditions of growth using the arca-arcb two-component signal transduction system. this system, in conjunction with other proteins, regulates the respiratory metabolic pathways in the organism. arca is a member of the ompr/phob subfamily of response regulator transcription factors that are known to regulate transcription by binding in tandem to target dna direct repeats. it is still unclear in this subfamily how activation by phosphoryl ... | 2005 | 15876365 |
| characterization of an archaeal malic enzyme from the hyperthermophilic archaeon thermococcus kodakaraensis kod1. | although the interconversion between c4 and c3 compounds has an important role in overall metabolism, limited information is available on the properties and regulation of enzymes acting on these metabolites in hyperthermophilic archaea. malic enzyme is one of the enzymes involved in this interconversion, catalyzing the oxidative decarboxylation of malate to pyruvate as well as the reductive carboxylation coupled with nad(p)h. this study focused on the enzymatic properties and expression profile ... | 2005 | 15876562 |
| recombinant production of zymomonas mobilis pyruvate decarboxylase in the haloarchaeon haloferax volcanii. | the unusual physiological properties of archaea (e.g., growth in extreme salt concentration, temperature and ph) make them ideal platforms for metabolic engineering. towards the ultimate goal of modifying an archaeon to produce bioethanol or other useful products, the pyruvate decarboxylase gene of zymomonas mobilis (zm pdc) was expressed in haloferax volcanii. this gene has been used successfully to channel pyruvate to ethanol in various gram-negative bacteria, including escherichia coli. altho ... | 2005 | 15876566 |
| recombinant production of zymomonas mobilis pyruvate decarboxylase in the haloarchaeon haloferax volcanii. | the unusual physiological properties of archaea (e.g., growth in extreme salt concentration, temperature and ph) make them ideal platforms for metabolic engineering. towards the ultimate goal of modifying an archaeon to produce bioethanol or other useful products, the pyruvate decarboxylase gene of zymomonas mobilis (zm pdc) was expressed in haloferax volcanii. this gene has been used successfully to channel pyruvate to ethanol in various gram-negative bacteria, including escherichia coli. altho ... | 2005 | 15876566 |
| genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. | bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (phx) genes and several genomic properties. there is a striking difference in the status of phx ribosomal protein (rp) genes where the archaeal genome generally encodes more rp genes and fewer phx rps compared with bacterial genomes. the increase in rps in archaea and eukaryotes compared with that in bacteria may reflect a more complex set of interactions in archaea and eukaryotes in regulating tr ... | 2005 | 15883367 |
| an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus. | dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ... | 2005 | 15886391 |
| rira is the iron response regulator of the rhizobactin 1021 biosynthesis and transport genes in sinorhizobium meliloti 2011. | the genes encoding the biosynthesis and transport of rhizobactin 1021, a siderophore produced by sinorhizobium meliloti, are negatively regulated by iron. mutagenesis of rira, the rhizobial iron regulator, resulted in abolition of the iron responsive regulation of the biosynthesis and transport genes. bioassay analysis revealed that the siderophore is produced in the presence of iron in a rira mutant. rna analysis and gfp fusions supported the conclusion that rira is the mediator of iron-respons ... | 2005 | 15899411 |
| bordetella alcs transporter functions in alcaligin siderophore export and is central to inducer sensing in positive regulation of alcaligin system gene expression. | bordetella pertussis and bordetella bronchiseptica, which are respiratory mucosal pathogens of mammals, produce and utilize the siderophore alcaligin to acquire iron in response to iron starvation. a predicted permease of the major facilitator superfamily class of membrane efflux pumps, alcs (synonyms, orfx and bcr), was reported to be encoded within the alcaligin gene cluster. in this study, alcs null mutants were found to be defective in growth under iron starvation conditions, in iron source ... | 2005 | 15901687 |
| novel molecular features of the fibrolytic intestinal bacterium fibrobacter intestinalis not shared with fibrobacter succinogenes as determined by suppressive subtractive hybridization. | suppressive subtractive hybridization was conducted to identify unique genes coding for plant cell wall hydrolytic enzymes and other properties of the gastrointestinal bacterium fibrobacter intestinalis dr7 not shared by fibrobacter succinogenes s85. subtractive clones from f. intestinalis were sequenced and assembled to form 712 nonredundant contigs with an average length of 525 bp. of these, 55 sequences were unique to f. intestinalis. the remaining contigs contained 764 genes with blastx simi ... | 2005 | 15901698 |
| 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 |
| a new system to control the barnase expression by a nifa-dependent promoter. | barnase is a potent ribonuclease widely used as a cytotoxic agent, tightly regulated by barstar to maintain cell viability. in this report, we describe a new composite regulatory system to control barnase cytotoxicity and expression, involving barstar and laci genes under control of the nifa-, sigma54-dependent sinorhizobium meliloti nifh promoter, and the barnase gene under control of the laci-repressible ptac promoter. in this system, expression of thenifh promoter, activated by constitutively ... | 2005 | 15908028 |
| deletion analysis of rhizobium meliloti symbiotic promoters. | previous examination of dna sequences located 5' to rhizobium meliloti nif transcription units has shown that extensive sequence homology exists among them. here we have examined these reiterated sequences for their role in symbiotic gene regulation. promoter deletion analysis has shown that although an extensive upstream dna sequence 9160 bp) is required for full heterologous activation of the r. meliloti nifhdk promoter by the klebsiella pneumoniae nifa protein in escherichia coli, this region ... | 1985 | 15929217 |
| expression of the nodulation gene nod c of rhizobium meliloti in escherichia coli: role of the nod c gene product in nodulation. | the nod c gene of rhizobium meliloti encodes a protein of mol. wt. 44 000 which is highly conserved in at least three rhizobium species. in order to overproduce this protein, a gene fusion of lambda ci repressor sequences to a large fragment of nod c was constructed. the fusion was placed under control of the tac promoter on plasmid pea305 to yield pjs1035. iptg-induced escherichia coli cells harbouring pjs1035 accumulated the ci-nod c hybrid protein up to 19% of total cellular protein. the synt ... | 1985 | 15929218 |
| 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 |
| complete nucleotide sequence of the le1 prophage from the spirochete leptospira biflexa and characterization of its replication and partition functions. | the first and, to date, only extrachromosomal circular replicon identified in the spirochete leptospira is the le1 prophage from leptospira biflexa. the 74-kb le1 genome has a gc content of 36%, which is similar to the gc content of leptospira spp. most of the 79 predicted open reading frames (orfs) showed no similarities to known orfs. however 21 orfs appeared to be organized in clusters that could code for head and tail structural proteins and immunity repressor proteins. in addition, the patt ... | 2005 | 15937155 |
| characterization of gla(kp), a udp-galacturonic acid c4-epimerase from klebsiella pneumoniae with extended substrate specificity. | in escherichia coli and salmonella enterica, the core oligosaccharide backbone of the lipopolysaccharide is modified by phosphoryl groups. the negative charges provided by these residues are important in maintaining the barrier function of the outer membrane. in contrast, klebsiella pneumoniae lacks phosphoryl groups in its core oligosaccharide but instead contains galacturonic acid residues that are proposed to serve a similar function in outer membrane stability. gla(kp) is a udp-galacturonic ... | 2005 | 15937173 |
| overproduction of ccmg and ccmfh(rc) fully suppresses the c-type cytochrome biogenesis defect of rhodobacter capsulatus ccmi-null mutants. | gram-negative bacteria like rhodobacter capsulatus use intertwined pathways to carry out the posttranslational maturation of c-type cytochromes (cyts). this periplasmic process requires at least 10 essential components for apo-cyt c chaperoning, thio-oxidoreduction, and the delivery of heme and its covalent ligation. one of these components, ccmi (also called cych), is thought to act as an apo-cyt c chaperone. in r. capsulatus, ccmi-null mutants are unable to produce c-type cyts and thus sustain ... | 2005 | 15937187 |
| recombinant pas-heme domains of oxygen sensing proteins: high level production and physical characterization. | details of a high-level recombinant production method for the heme-pas domains of heme oxygen sensing proteins from sinorhizobium meliloti (sm) (formerly rhizobium meliloti, rm), bradyrhizobium japonicum (bj), and escherichia coli (ec) are described. using a newly proposed, concise, and unambiguous naming system (also described here) these proteins are: smfixlh(128-264), bjfixlh(140-270), and ecdosh(1-147). in addition, high-level production of bjfixl(140-505), the soluble full-length protein co ... | 2005 | 15939306 |
| the tetr family of transcriptional repressors. | we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ... | 2005 | 15944459 |
| role of oxyr from sinorhizobium meliloti in regulating the expression of catalases. | the process of symbiotic nitrogen fixation results in the generation of reactive oxygen species such as the superoxide anion (o2-) and hydrogen peroxide (h2o2). the response of rhizobia to these toxic oxygen species is an important factor in nodulation and nitrogen fixation. in sinorhizobium meliloti, one oxyr homologue and three catalase genes, kata, katb, and katc were detected by sequence analysis. this oxyr gene is located next to and divergently from kata on the chromosome. to investigate t ... | 2005 | 15944758 |
| 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 |
| evasion of toll-like receptor 5 by flagellated bacteria. | toll-like receptor 5 (tlr5) recognizes an evolutionarily conserved site on bacterial flagellin that is required for flagellar filament assembly and motility. the alpha and epsilon proteobacteria, including the important human pathogens campylobacter jejuni, helicobacter pylori, and bartonella bacilliformis, require flagellar motility to efficiently infect mammalian hosts. in this study, we demonstrate that these bacteria make flagellin molecules that are not recognized by tlr5. we map the site r ... | 2005 | 15956202 |
| 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 |
| production of glucuronan oligosaccharides using a new glucuronan lyase activity from a trichoderma sp. strain. | sinorhizobium meliloti m5n1cs synthesizes a homopolymer of glucuronic acids beta-(1,4) linked and variably c2 and/or c3o-acetylated. to obtain beta-delta-(4,5)-unsaturated oligoglucuronans, various acetylated forms of this bacterial polymer were cleaved by a trichoderma sp. gl2 glucuronan lyase. oligomers with polymerization degrees up to 8 were then produced, purified by liquid chromatography (size exclusion and anions exchange) and characterized using 1h nmr and esi-q/tof-ms. finally, the prod ... | 2005 | 15961175 |
| the pleiotropic nature of symbiotic regulatory mutants: bradyrhizobium japonicum nifa gene is involved in control of nif gene expression and formation of determinate symbiosis. | in the slow-growing soybean symbiont, bradyrhizobium japonicum (strain 110), a nifa-like regulatory gene was located immediately upstream of the previously mapped fixa gene. by interspecies hybridization and partial dna sequencing the gene was found to be homologous to nifa from klebsiella pneumoniae and rhizobium meliloti, and to a lesser extent, also to ntrc from k. pneumoniae. the b. japonicum nifa gene product was shown to activate b. japonicum and k. pneumoniae nif promoters (using nif::lac ... | 1986 | 15966104 |
| characterization of a bifunctional puta homologue from bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor. | puta is a bifunctional flavoenzyme in bacteria that catalyzes the four-electron oxidation of proline to glutamate. in certain prokaryotes such as escherichia coli, puta is also a transcriptional repressor of the proline utilization (put) genes and thus is trifunctional. in this work, we have begun to assess differences between bifunctional and trifunctional puta enzymes by examining the puta protein from bradyrhizobium japonicum (bjputa). primary structure analysis of bjputa shows it lacks the d ... | 2005 | 15966737 |
| pyd genes of rhizobium sp. strain tal1145 are required for degradation of 3-hydroxy-4-pyridone, an aromatic intermediate in mimosine metabolism. | rhizobium sp. strain tal1145 degrades the leucaena toxin mimosine and its degradation product 3-hydroxy-4-pyridone (hp). the aim of this investigation is to characterize the rhizobium genes for hp degradation and transport. these genes were localized by subcloning and mutagenesis on a previously isolated cosmid, puhr263, containing mid genes of tal1145 required for mimosine degradation. two structural genes, pyda and pydb, encoding a metacleavage dioxygenase and a hydrolase, respectively, are re ... | 2005 | 15968058 |
| phenylacetate catabolism in rhodococcus sp. strain rha1: a central pathway for degradation of aromatic compounds. | in gram-negative bacteria, a pathway for aerobic degradation of phenylacetic acid (paa) that proceeds via phenylacetyl-coenzyme a (coa) and hydrolytic ring fission plays a central role in the degradation of a range of aromatic compounds. in contrast, the paa pathway and its role are not well characterized in gram-positive bacteria. a cluster including 13 paa genes encoding enzymes orthologous to those of gram-negative bacteria was identified on the chromosome of rhodococcus sp. strain rha1. thes ... | 2005 | 15968060 |
| two new sinorhizobium meliloti lysr-type transcriptional regulators required for nodulation. | the establishment of an effective nitrogen-fixing symbiosis between sinorhizobium meliloti and its legume host alfalfa (medicago sativa) depends on the timely expression of nodulation genes that are controlled by lysr-type regulators. ninety putative genes coding for lysr-type transcriptional regulators were identified in the recently sequenced s. meliloti genome. all 90 putative lysr genes were mutagenized using plasmid insertions as a first step toward determining their roles in symbiosis. two ... | 2005 | 15968067 |
| inactivation of the pst system reduces the virulence of an avian pathogenic escherichia coli o78 strain. | escherichia coli o78 strains are frequently associated with extraintestinal diseases, such as airsacculitis and septicemia, in poultry, livestock, and humans. to understand the influence of the pst operon in the virulence of e. coli, we introduced mutations into the pst genes of the avian pathogenic e. coli (apec) o78:k80 strain chi7122 by allelic exchange. the mutation of pst genes led to the constitutive expression of the pho regulon. furthermore, the virulence of apec strain chi7122 in a chic ... | 2005 | 15972503 |
| differential gene expression in benznidazole-resistant trypanosoma cruzi parasites. | we analyzed the differential gene expression among representative trypanosoma cruzi stocks in relation to benznidazole exposures using a random differentially expressed sequences (rades) technique. studies were carried out with drug pressure both at the natural susceptibility level of the wild-type parasite (50% inhibitory concentration for the wild type) and at different resistance levels. the pattern of differential gene expression performed with resistant stocks was compared to the population ... | 2005 | 15980339 |
| brigep--the bridge-based genome-transcriptome-proteome browser. | the growing amount of information resulting from the increasing number of publicly available genomes and experimental results thereof necessitates the development of comprehensive systems for data processing and analysis. in this paper, we describe the current state and latest developments of our brigep bioinformatics software system consisting of three web-based applications: gendb, emma and prodb. these applications facilitate the processing and analysis of bacterial genome, transcriptome and ... | 2005 | 15980569 |
| the mrp system: a giant among monovalent cation/proton antiporters? | mrp systems are a novel and broadly distributed type of monovalent cation/proton antiporter of bacteria and archaea. monovalent cation/proton antiporters are membrane transport proteins that catalyze efflux of cytoplasmic sodium, potassium or lithium ions in exchange for external hydrogen ions (protons). other known monovalent cation antiporters are single gene products, whereas mrp systems have been proposed to function as hetero-oligomers. a mrp operon typically has six or seven genes encoding ... | 2005 | 15980940 |
| the latd gene of medicago truncatula is required for both nodule and root development. | the evolutionary origins of legume root nodules are largely unknown. we have identified a gene, latd, of the model legume medicago truncatula, that is required for both nodule and root development, suggesting that these two developmental processes may share a common evolutionary origin. the latd mutant plants initiate nodule formation but do not complete it, resulting in immature, non-nitrogen-fixing nodules. similarly, lateral roots initiate, but remain short stumps. the primary root, which ini ... | 2005 | 15986921 |
| [transcriptional regulation of noeab from sinorhizobium meliloti 042bm]. | the expression regulation of s. meliloti 042bm noeab was studied. the results showed that trigonelline could not elevate the level of noeab expression, which indicated that these genes are not regulated by nodd2. since association of nodd3 and syrm could not change the level of the genes expression, they aren't also controlled by nodd3-syrm system. however, induction of luteolin resulted in 16 times increase of noeab expression, which indicated that noeab was regulated by nodd1. most interesting ... | 2005 | 15989222 |
| [the expression of gene related to salt tolerance from sinorhizobium meliloti 042bm in escherichia coli and purification of its fusion protein]. | a 1.9kb dna fragment related to salt tolerance of s. meliloti strain 042bm containing two open reading frames were obtained by pcr amplification and ligated into shuttle vector pbbr1-mcs2. the complementation experiment showed that orf2 is related to salt tolerance and named as rsta gene. then the gene was cloned into the expression vector pthio-hisa, b and c, respectively, and recombinant expression vectors pgsa, pgb and pgc were constructed, and transformed into e. coli top10. inducing by iptg ... | 2005 | 15989246 |
| [cloning, deletion and functional analysis of noea from sinorhizobium meliloti 042bm]. | 042bm noea was obtained by pcr. it is identical to that of s. meliloti 1021 at 99% level, and similarity of their noea is 97%. in addition, it was found that this protein shares significant homology with the sam-dependent methyltransferase of mesorhizobium sp. bnc1 (32% similarity), and the similarity of its 303-362 region to the 160- 220 region of ll11 methyltransferases of e. coli (prma) is 41%. compared to 042bm, the noea deletion mutant 042bma-km showed different degrees of increase in numbe ... | 2005 | 15989259 |
| citrate synthase mutants of agrobacterium are attenuated in virulence and display reduced vir gene induction. | a citrate synthase (cs) deletion mutant of agrobacterium tumefaciens c58 is highly attenuated in virulence. the identity of the mutant was initially determined from its amino acid sequence, which is 68% identical to escherichia coli and 77% identical to brucella melitensis. the mutant lost all cs enzymatic activity, and a cloned cs gene complemented a cs mutation in sinorhizobium. the cs mutation resulted in a 10-fold reduction in vir gene expression, which likely accounts for the attenuated vir ... | 2005 | 15995199 |
| functional and topological analysis of the burkholderia cenocepacia priming glucosyltransferase bceb, involved in the biosynthesis of the cepacian exopolysaccharide. | the bceb protein of the cystic fibrosis mucoid isolate burkholderia cenocepacia ist432 is proposed to catalyze the first step of the exopolysaccharide repeat unit assembly. extracts of escherichia coli cells overexpressing bceb were shown to contain glycosyltransferase activity and mediate incorporation of glucose-1-phosphate into membrane lipids. the amino acid sequence of bceb exhibits two conserved regions, one comprising two invariant aspartic acid residues (asp339 and asp355) that are essen ... | 2005 | 15995219 |
| analysis and update of the human aldehyde dehydrogenase (aldh) gene family. | the aldehyde dehydrogenase (aldh) gene superfamily encodes enzymes that are critical for certain life processes and detoxification via the nad(p)(+)-dependent oxidation of numerous endogenous and exogenous aldehyde substrates, including pharmaceuticals and environmental pollutants. analysis of the aldh gene superfamily in the latest databases showed that the human genome contains 19 putatively functional genes and three pseudogenes. a number of aldh genes are upregulated as a part of the oxidati ... | 2005 | 16004729 |
| formation of organelle-like n2-fixing symbiosomes in legume root nodules is controlled by dmi2. | in most legume nodules, the n2-fixing rhizobia are present as organelle-like structures inside their host cells. these structures, named symbiosomes, contain one or a few rhizobia surrounded by a plant membrane. symbiosome formation requires the release of bacteria from cell-wall-bound infection threads. in primitive legumes, rhizobia are hosted in intracellular infection threads that, in contrast to symbiosomes, are bound by a cell wall. the formation of symbiosomes is presumed to represent a m ... | 2005 | 16006515 |
| a conserved mechanism for sulfonucleotide reduction. | sulfonucleotide reductases are a diverse family of enzymes that catalyze the first committed step of reductive sulfur assimilation. in this reaction, activated sulfate in the context of adenosine-5'-phosphosulfate (aps) or 3'-phosphoadenosine 5'-phosphosulfate (paps) is converted to sulfite with reducing equivalents from thioredoxin. the sulfite generated in this reaction is utilized in bacteria and plants for the eventual production of essential biomolecules such as cysteine and coenzyme a. hum ... | 2005 | 16008502 |
| soil nematodes mediate positive interactions between legume plants and rhizobium bacteria. | symbiosis between legume species and rhizobia results in the sequestration of atmospheric nitrogen into ammonium, and the early mechanisms involved in this symbiosis have become a model for plant-microbe interactions and thus highly amenable for agricultural applications. the working model for this interaction states that the symbiosis is the outcome of a chemical/molecular dialogue initiated by flavonoids produced by the roots of legumes and released into the soil as exudates, which specificall ... | 2005 | 16025342 |
| the stringent response is required for amino acid and nitrate utilization, nod factor regulation, nodulation, and nitrogen fixation in rhizobium etli. | a rhizobium etli tn5 insertion mutant, lm01, was selected for its inability to use glutamine as the sole carbon and nitrogen source. the tn5 insertion in lm01 was localized to the rsh gene, which encodes a member of the rela/spot family of proteins. the lm01 mutant was affected in the ability to use amino acids and nitrate as nitrogen sources and was unable to accumulate (p)ppgpp when grown under carbon and nitrogen starvation, as opposed to the wild-type strain, which accumulated (p)ppgpp under ... | 2005 | 16030199 |
| characterization of a multigene-encoded sodium/hydrogen antiporter (sha) from pseudomonas aeruginosa: its involvement in pathogenesis. | sha (also known as mrp/mnh/pha) is a na+/h+ antiporter encoded by a cluster of six or seven genes that probably form a multisubunit transport complex. the sha system is important for the homeostasis of h+, na+, and other monovalent cations and plays a critical role in various functions, including alkaliphily, sporulation, and symbiosis. here, we characterized the sha homologue genes from the opportunistic pathogen pseudomonas aeruginosa, which exist as a cluster of six genes (pa1054 to pa1059). ... | 2005 | 16030218 |
| unusual group ii introns in bacteria of the bacillus cereus group. | a combination of sequence and structure analysis and reverse transcriptase pcr experiments was used to characterize the group ii introns in the complete genomes of two strains of the pathogen bacillus cereus. while b. cereus atcc 14579 harbors a single intron element in the chromosome, b. cereus atcc 10987 contains three introns in the chromosome and four in its 208-kb pbc10987 plasmid. the most striking finding is the presence in b. cereus atcc 10987 of an intron [b.c.i2(a)] located on the reve ... | 2005 | 16030238 |
| effective symbiosis between rhizobium etli and phaseolus vulgaris requires the alarmone ppgpp. | the symbiotic interaction between rhizobium etli and phaseolus vulgaris, the common bean plant, ultimately results in the formation of nitrogen-fixing nodules. many aspects of the intermediate and late stages of this interaction are still poorly understood. the r. etli rela gene was identified through a genome-wide screening for r. etli symbiotic mutants. rela has a pivotal role in cellular physiology, as it catalyzes the synthesis of (p)ppgpp, which mediates the stringent response in bacteria. ... | 2005 | 16030240 |
| de novo alanine synthesis by bacteroids of mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of lotus corniculatus. | deletion of both alanine dehydrogenase genes (alda) in mesorhizobium loti resulted in the loss of alda enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of lotus corniculatus plants. thus, neither indeterminate pea nodules nor determinate l. corniculatus nodules export alanine as the sole nitrogen secretion product. | 2005 | 16030244 |
| role of trehalose transport and utilization in sinorhizobium meliloti--alfalfa interactions. | genes thua and thub in sinorhizobium meliloti rm1021 code for a major pathway for trehalose catabolism and are induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. s. meliloti strains mutated in either of these two genes were severely impaired in their ability to grow on trehalose as the sole source of carbon. thua and thub show no homology to any known enzymes in trehalose utilization. thua has similarity to proteins of unknown function in mesorhiz ... | 2005 | 16042015 |
| guab activity is required in rhizobium tropici during the early stages of nodulation of determinate nodules but is dispensable for the sinorhizobium meliloti-alfalfa symbiotic interaction. | the guab mutant strain rhizobium tropici ciat8999-10t is defective in symbiosis with common bean, forming nodules that lack rhizobial content. in order to investigate the timing of the guab requirement during the nodule formation on the host common bean by the strain ciat899-10.t, we constructed gene fusions in which the guab gene is expressed under the control of the symbiotic promoters noda, baca, and nifh. our data indicated that the guab is required from the early stages of nodulation becaus ... | 2005 | 16042020 |
| the lipopolysaccharide of brucella abortus bvrs/bvrr mutants contains lipid a modifications and has higher affinity for bactericidal cationic peptides. | the two-component bvrs/bvrr system is essential for brucella abortus virulence. it was shown previously that its dysfunction abrogates expression of some major outer membrane proteins and increases bactericidal peptide sensitivity. here, we report that bvrs/bvrr mutants have increased surface hydrophobicity and susceptibility to killing by nonimmune serum. the bvrs and bvrr mutant lipopolysaccharides (lpss) bound more polymyxin b, chimeras constructed with bvrs mutant cells and parental lps show ... | 2005 | 16077108 |
| flig subunit arrangement in the flagellar rotor probed by targeted cross-linking. | flig is a component of the switch complex on the rotor of the bacterial flagellum. each flagellar motor contains about 25 flig molecules. the protein of escherichia coli has 331 amino acid residues and comprises at least two discrete domains. a c-terminal domain of about 100 residues functions in rotation and includes charged residues that interact with the stator protein mota. other parts of the flig protein are essential for flagellar assembly and interact with the ms ring protein flif and the ... | 2005 | 16077109 |
| carboxyl-terminal protease regulates brucella suis morphology in culture and persistence in macrophages and mice. | the putative carboxyl-terminal processing protease (ctpa) of brucella suis 1330 is a member of a novel family of endoproteases involved in the maturation of proteins destined for the cell envelope. the b. suis ctpa protein shared up to 77% homology with ctpa proteins of other bacteria. a ctpa-deficient brucella strain (1330deltactpa), generated by allelic exchange, produced smaller colonies on enriched agar plates and exhibited a 50% decrease in growth rate in enriched liquid medium and no growt ... | 2005 | 16077124 |
| genome wide identification of dna binding motifs of nodd-factor in sinorhizobium meliloti and mesorhizobium loti. | nodd transcription factor is a regulatory protein of nitrogen fixing bacteria, which activates expression of nod genes participating in nodulation during interaction with its symbiont legumes. it's dna binding motifs have been characterized and reported in sinorhizobium meliloti and this pattern information has been used in our theoretical analyses to detect its novel regulated genes in genomes of s. meliloti and mesorhizobium loti. m. loti, a symbiont to model legume plant lotus japonicus, show ... | 2005 | 16078361 |
| expression of nitrite and nitric oxide reductases in free-living and plant-associated agrobacterium tumefaciens c58 cells. | a number of the bacteria that form associations with plants are denitrifiers. to learn more about how the association with plants affects expression of denitrification genes, the regulation of nitrite and nitric oxide reductases was investigated in agrobacterium tumefaciens. analysis of free-living cells revealed that expression of the genes encoding nitrite and nitric oxide reductases, nirk and nor, respectively, requires low-oxygen conditions, nitric oxide, and the transcriptional regulator nn ... | 2005 | 16085833 |
| proteins encoded by sphingomonas elodea atcc 31461 rmla and ugpg genes, involved in gellan gum biosynthesis, exhibit both dtdp- and udp-glucose pyrophosphorylase activities. | the commercial gelling agent gellan is a heteropolysaccharide produced by sphingomonas elodea atcc 31461. in this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmla) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dtdp-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan ... | 2005 | 16085866 |
| transcriptome-based identification of the sinorhizobium meliloti nodd1 regulon. | the nodd1 regulon of sinorhizobium meliloti was determined through the analysis of the s. meliloti transcriptome in response to the plant flavone luteolin and the overexpression of nodd1. nine new genes regulated by both nodd1 and luteolin were identified, demonstrating that nodd1 controls few functions behind nodulation in s. meliloti. | 2005 | 16085895 |
| evidence for a second class of s-adenosylmethionine riboswitches and other regulatory rna motifs in alpha-proteobacteria. | riboswitches are rna elements in the 5' untranslated leaders of bacterial mrnas that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. riboswitches are most common in the genomes of low gc gram-positive bacteria (for example, bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group. | 2005 | 16086852 |
| properties of motility in bacillus subtilis powered by the h+-coupled motab flagellar stator, na+-coupled motps or hybrid stators motas or motpb. | bacillus subtilis has a single set of flagellar rotor proteins that interact with two distinct stator-force generators, the h+-coupled motab complex and the na+-coupled motps complex, that energize rotation. here, motility on soft agar plates and in liquid was assayed in wild-type b.subtilis and strains expressing only one stator, either motab, motps or hybrid motas or motpb. the strains expressing motab or motas had an average of 11 flagella/cell while those expressing motps or motpb had an ave ... | 2005 | 16095621 |
| peptide mass mapping of acetylated isoforms of histone h4 from mouse lymphosarcoma cells treated with histone deacetylase (hdacs) inhibitors. | the acetylated isoforms of histone h4 from mouse lymphosarcoma cells treated with hdac inhibitors trichostatin a (tsa) and depsipeptide (ddp) were separated by acetic acid urea-polyacrylamide gel electrophoresis (au-page), in-gel digested, and analyzed by matrix assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms) and liquid chromatography tandem mass spectrometry (lc-ms/ms). the acetylation pattern of histone h4 in mouse lymphosarcoma cells induced by tsa was est ... | 2005 | 16099169 |
| the rhizobium etli biomny operon is involved in biotin transport. | because rhizobium etli ce3 is normally dependent on an external source of biotin and lacks orthodox biotin biosynthesis genes, we undertook an analysis of biotin uptake in this organism. by complementation of a sinorhizobium meliloti biom mutant we isolated an r. etli chromosomal region encoding homologs of the s. meliloti biomnb genes, whose products have been implicated in intracellular biotin retention in that organism. disruption of the r. etli biom resulted in a mutant which took up biotin ... | 2005 | 16099603 |
| e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects. | the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ... | 2005 | 16109942 |
| phosphoenolpyruvate carboxykinase is an acid-induced, chromosomally encoded virulence factor in agrobacterium tumefaciens. | the pcka gene, encoding phosphoenolpyruvate carboxykinase, catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to form phosphoenolpyruvate. located on the circular chromosome of agrobacterium, this locus is adjacent to the loci chvg and chvi, encoding a two-component regulatory system that has been shown to be important in virulence. using a reporter gene fusion, studies showed that the pcka gene is induced by acidic ph but not by acetosyringone. this acid induction is r ... | 2005 | 16109945 |
| xanthomonas campestris pv. campestris possesses a single gluconeogenic pathway that is required for virulence. | disruption of ppsa, a key gene in gluconeogenesis, of xanthomonas campestris pv. campestris resulted in the failure of the pathogen to grow in medium with pyruvate or c4-dicarboxylates as the sole carbon source and a significant reduction in virulence, indicating that x. campestris pv. campestris possesses only the malic enzyme-ppsa route in gluconeogenesis, which is required for virulence. | 2005 | 16109965 |
| [a sinorhizoboium meliloti strain that can nodulate soybean plants]. | sinorhizobium meliloti xj96077 was isolated from root nodules of alfalfa (medicago sativa) in xinjiang region of china. nodulation experiments showed that both soybean and alfalfa were effectively nodulated by xj96077. the dna (g+ c) mol% of strain xj96077 was 61.9%. the dna homologies of strain xj96077 were 93% and 80% with s. meliloti usda1002t and 042bm, respectively. these results showed that xj96077 belongs to sinorhizobium meliloti. to prove the capability of xj96077 to nodulate both soybe ... | 2004 | 16110948 |
| systematic targeted mutagenesis of brucella melitensis 16m reveals a major role for gntr regulators in the control of virulence. | in order to identify transcriptional regulators involved in virulence gene control in brucella melitensis, we generated a collection of 88 mutants in the arac, arsr, crp, deor, gntr, iclr, lysr, merr, rpir, and tetr families of regulators. this collection was named limur (library of mutants for regulators). we developed a method to test several mutants simultaneously in one animal in order to identify those unable to survive. this method, called the plasmid-tagged mutagenesis method, was used to ... | 2005 | 16113274 |
| characterization of the dapa-nlpb genetic locus involved in regulation of swarming motility, cell envelope architecture, hemolysin production, and cell attachment ability in serratia marcescens. | swarming migration of serratia marcescens requires both flagellar motility and cellular differentiation and is a population-density-dependent behavior. while the flhdc and quorum-sensing systems have been characterized as important factors regulating s. marcescens swarming, the underlying molecular mechanisms are currently far from being understood. serratia swarming is thermoregulated and is characterized by continuous surface migration on rich swarming agar surfaces at 30 degrees c but not at ... | 2005 | 16113328 |
| individual subunits of the glutamate transporter eaac1 homotrimer function independently of each other. | glutamate transporters are thought to be assembled as trimers of identical subunits that line a central hole, possibly the permeation pathway for anions. here, we have tested the effect of multimerization on the transporter function. to do so, we coexpressed eaac1(wt) with the mutant transporter eaac1(r446q), which transports glutamine but not glutamate. application of 50 microm glutamate or 50 microm glutamine to cells coexpressing similar numbers of both transporters resulted in anion currents ... | 2005 | 16128593 |
| expression of the medicago truncatula dm12 gene suggests roles of the symbiotic nodulation receptor kinase in nodules and during early nodule development. | the medicago truncatula dmi2 gene encodes a receptorlike kinase required for establishing root endosymbioses. the dmi2 gene was shown to be expressed much more highly in roots and nodules than in leaves and stems. in roots, its expression was not altered by nitrogen starvation or treatment with lipochitooligosaccharidic nod factors. moreover, the dmi2 mrna abundance in roots of the nfp, dmil, dmi3, nsp1, nsp2, and hcl symbiotic mutants was similar to the wild type, whereas lower levels in some d ... | 2005 | 16134899 |
| new gammaproteobacteria associated with blood-feeding leeches and a broad phylogenetic analysis of leech endosymbionts. | many monophagous animals have coevolutionary relationships with bacteria that provide unavailable nutrients to the host. frequently, these microbial partners are vertically inherited and reside in specialized structures or tissues. here we report three new lineages of bacterial symbionts of blood-feeding leeches, one from the giant amazonian leech, haementeria ghilianii, and two others from placobdelloides species. these hosts each possess a different mycetome or esophageal organ morphology wher ... | 2005 | 16151107 |
| identification of genes induced in listeria monocytogenes during growth and attachment to cut cabbage, using differential display. | the food-borne pathogen listeria monocytogenes is a ubiquitous soil bacterium with the potential to contaminate fresh produce during cultivation and postharvest processing. in order to identify potential mechanisms by which l. monocytogenes may successfully attach to and colonize fresh produce, gene expression in l. monocytogenes cells inoculated onto fresh-cut cabbage was compared to gene expression in cells grown under control conditions. differential display of reverse transcriptase pcr fragm ... | 2005 | 16151109 |